Well, dont know what to really make of this, ive been having trouble with it all night.
It seems i cant mplex my ac3 audio which has been extracted from a vob file with my video m2v file also coming from the same vob... mplex doesnt seem to recognize the ac3 format, although i have tried with a different audio track " tcextract [...] -a 9 " which is DTS audio and mplex allows the multiplexing to go ahead...

On the other hand, tcmplex gives me no problem and allows the multiplexing.

Is this a bug with mplex?

what is weird is that i could get the ac3 mplexed with my m2v no problem on the first vob file, then the second and third and .... is a no go.

here is the output of tcprobe for the first four vob files: and lower down the mplex and tcmplex situation with the ac3 file which has been extracted from the fourth vob file with tcextract.

/****************************************/
pat@anus ~ $ tcprobe -i /mnt/cdrom/video_ts/vts_01_1.vob
[tcprobe] MPEG program stream (PS)
[tcprobe] summary for /mnt/cdrom/video_ts/vts_01_1.vob, (*) = not default, 0 = not detected
import frame size: -g 720x480 [720x576] (*)
aspect ratio: 16:9 (*)
frame rate: -f 23.976 [25.000] frc=1 (*)
PTS=0.2806, frame_time=41 ms, bitrate=9800 kbps
audio track: -a 0 [0] -e 48000,16,3 [48000,16,2] -n 0x2000 [0x2000] (*)
PTS=0.2806, bitrate=448 kbps
-D 0 --av_fine_ms 0 (frames & ms) [0] [0]
audio track: -a 2 [0] -e 48000,16,3 [48000,16,2] -n 0x2000 [0x2000] (*)
PTS=0.2806, bitrate=384 kbps
-D 0 --av_fine_ms 0 (frames & ms) [0] [0]
audio track: -a 3 [0] -e 48000,16,2 [48000,16,2] -n 0x2000 [0x2000]
PTS=0.2806, bitrate=384 kbps
-D 0 --av_fine_ms 0 (frames & ms) [0] [0]
audio track: -a 9 [0] -e 48000,16,5 [48000,16,2] -n 0x1000f [0x2000] (*)
PTS=0.2806, bitrate=768 kbps
-D 0 --av_fine_ms 0 (frames & ms) [0] [0]
pat@anus ~ $ tcprobe -i /mnt/cdrom/video_ts/vts_01_2.vob
[tcprobe] MPEG program stream (PS)
[tcprobe] summary for /mnt/cdrom/video_ts/vts_01_2.vob, (*) = not default, 0 = not detected
import frame size: -g 720x480 [720x576] (*)
aspect ratio: 16:9 (*)
frame rate: -f 23.976 [25.000] frc=1 (*)
PTS=985.1812, frame_time=41 ms, bitrate=9800 kbps
audio track: -a 0 [0] -e 48000,16,2 [48000,16,2] -n 0x2000 [0x2000]
PTS=984.9526, bitrate=448 kbps
-D 5 --av_fine_ms 20 (frames & ms) [0] [0]
audio track: -a 2 [0] -e 48000,16,3 [48000,16,2] -n 0x2000 [0x2000] (*)
PTS=984.9526, bitrate=56 kbps
-D 5 --av_fine_ms 20 (frames & ms) [0] [0]
audio track: -a 3 [0] -e 48000,16,2 [48000,16,2] -n 0x2000 [0x2000]
PTS=984.9846, bitrate=384 kbps
-D 4 --av_fine_ms 29 (frames & ms) [0] [0]
audio track: -a 9 [0] -e 48000,16,5 [48000,16,2] -n 0x1000f [0x2000] (*)
PTS=984.8353, bitrate=768 kbps
-D 8 --av_fine_ms 12 (frames & ms) [0] [0]
pat@anus ~ $ tcprobe -i /mnt/cdrom/video_ts/vts_01_3.vob
[tcprobe] MPEG program stream (PS)
[tcprobe] summary for /mnt/cdrom/video_ts/vts_01_3.vob, (*) = not default, 0 = not detected
import frame size: -g 720x480 [720x576] (*)
aspect ratio: 16:9 (*)
frame rate: -f 23.976 [25.000] frc=1 (*)
PTS=2000.1952, frame_time=41 ms, bitrate=9800 kbps
audio track: -a 0 [0] -e 48000,16,2 [48000,16,2] -n 0x2000 [0x2000]
PTS=1999.9926, bitrate=448 kbps
-D 4 --av_fine_ms 35 (frames & ms) [0] [0]
audio track: -a 2 [0] -e 48000,16,2 [48000,16,2] -n 0x2000 [0x2000]
PTS=2000.0246, bitrate=384 kbps
-D 4 --av_fine_ms 3 (frames & ms) [0] [0]
audio track: -a 3 [0] -e 48000,16,2 [48000,16,2] -n 0x2000 [0x2000]
PTS=2000.0246, bitrate=384 kbps
-D 4 --av_fine_ms 3 (frames & ms) [0] [0]
audio track: -a 9 [0] -e 48000,16,5 [48000,16,2] -n 0x1000f [0x2000] (*)
PTS=1999.8540, bitrate=768 kbps
-D 8 --av_fine_ms 7 (frames & ms) [0] [0]
pat@anus ~ $ tcprobe -i /mnt/cdrom/video_ts/vts_01_4.vob
[tcprobe] MPEG program stream (PS)
[tcprobe] summary for /mnt/cdrom/video_ts/vts_01_4.vob, (*) = not default, 0 = not detected
import frame size: -g 720x480 [720x576] (*)
aspect ratio: 16:9 (*)
frame rate: -f 23.976 [25.000] frc=1 (*)
PTS=3013.0404, frame_time=41 ms, bitrate=9800 kbps
audio track: -a 0 [0] -e 48000,16,2 [48000,16,2] -n 0x2000 [0x2000]
PTS=3012.7926, bitrate=448 kbps
-D 5 --av_fine_ms 39 (frames & ms) [0] [0]
audio track: -a 2 [0] -e 48000,16,2 [48000,16,2] -n 0x2000 [0x2000]
PTS=3012.8246, bitrate=384 kbps
-D 5 --av_fine_ms 7 (frames & ms) [0] [0]
audio track: -a 3 [0] -e 48000,16,2 [48000,16,2] -n 0x2000 [0x2000]
PTS=3012.7926, bitrate=384 kbps
-D 5 --av_fine_ms 39 (frames & ms) [0] [0]
audio track: -a 9 [0] -e 48000,16,5 [48000,16,2] -n 0x1000f [0x2000] (*)
PTS=3012.6966, bitrate=768 kbps
-D 8 --av_fine_ms 10 (frames & ms) [0] [0]
detected (2) subtitle(s)
/****************************************/
/****************************************/
/****************************************/

pat@anus ~/dvd/ $ mplayer temp/vts04.ac3
MPlayer 1.0pre6-3.4.3 (C) 2000-2004 MPlayer Team
CPU: Advanced Micro Devices (Family: 8, Stepping: 0)
Detected cache-line size is 64 bytes
Cannot test OS support for SSE, disabling to be safe.

Warning unknown option cache_min at line 144
Warning unknown option cache_prefill at line 147

77 audio & 189 video codecs
Playing temp/vts04.ac3.
XMMS: found plugin: libmpg123.so (MPEG Layer 1/2/3 Player 1.2.10)
XMMS: found plugin: libxmmsmad.so (MAD MPEG Decoder plugin 0.8)
XMMS: Closing plugin /usr/lib64/xmms/Input/libxmmsmad.so
XMMS: Closing plugin /usr/lib64/xmms/Input/libmpg123.so
libavformat file format detected.
==========================================================================
Opening audio decoder: [liba52] AC3 decoding with liba52
No accelerated IMDCT transform found
AC3: 5.1 (3f+2r+lfe) 48000 Hz 448.0 kbit/s
No accelerated resampler found
AUDIO: 48000 Hz, 2 ch, 16 bit (0x10), ratio: 56000->192000 (448.0 kbit)
Selected audio codec: [a52] afm:liba52 (AC3-liba52)
==========================================================================
Checking audio filter chain for 48000Hz/2ch/16bit -> 48000Hz/2ch/16bit...
AF_pre: af format: 2 bps, 2 ch, 48000 hz, little endian signed int
AF_pre: 48000Hz 2ch Signed 16-bit (Little-Endian)
AO: [oss] 48000Hz 2ch Signed 16-bit (Little-Endian) (2 bps)
Building audio filter chain for 48000Hz/2ch/16bit -> 48000Hz/2ch/16bit...
Video: no video
Starting playback...
A: 17.0 (17.0) 0.7% 45%

MPlayer interrupted by signal 2 in module: play_audio
pat@anus ~/dvd/ $ mplex -f 8 -o temp/vts04.mpg temp/vts04.m2v temp/vts04.ac3
INFO: [mplex] mplex version 1.6.2 (2.2.3 $Date: 2004/01/13 20:45:26 $)
INFO: [mplex] File temp/vts04.m2v looks like an MPEG Video stream.
**ERROR: [mplex] File unrecogniseable!
**ERROR: [mplex] Unrecogniseable file(s)... exiting.
pat@anus ~/dvd/ $ mplex -f 8 -o temp/vts04.mpg temp/vts04.m2v temp/vts04.ac3
INFO: [mplex] mplex version 1.6.2 (2.2.3 $Date: 2004/01/13 20:45:26 $)
INFO: [mplex] File temp/vts04.m2v looks like an MPEG Video stream.
**ERROR: [mplex] File unrecogniseable!
**ERROR: [mplex] Unrecogniseable file(s)... exiting.
pat@anus ~/dvd/ $ mplex -f 8 -o temp/vts04.mpg temp/vts04.ac3 temp/vts04.m2v
INFO: [mplex] mplex version 1.6.2 (2.2.3 $Date: 2004/01/13 20:45:26 $)
**ERROR: [mplex] File cQ unrecogniseable!
INFO: [mplex] File temp/vts04.m2v looks like an MPEG Video stream.
**ERROR: [mplex] Unrecogniseable file(s)... exiting.
pat@anus ~/dvd/ $ mplex -f 8 -o temp/vts04.mpg temp/vts04.m2v temp/vts.ac3
INFO: [mplex] mplex version 1.6.2 (2.2.3 $Date: 2004/01/13 20:45:26 $)
INFO: [mplex] File temp/vts04.m2v looks like an MPEG Video stream.
**ERROR: [mplex] File unrecogniseable!
**ERROR: [mplex] Unrecogniseable file(s)... exiting.
pat@anus ~/dvd/ $ mv temp/vts.ac3 temp/vts04.ac3
pat@anus ~/dvd/ $ tcmplex
tcmplex (transcode v0.6.14) (C) 2001 Thomas Oestreich

Usage: tcmplex [options] [-]
-i name video stream filename
-p name audio stream (track 0) filename
-s name audio stream (track 1) filename (optional)
-o name muliplexed program/system stream filename
-m mode predefined settings [1]
1 = mpeg1 vbr, buffer 46Kb (*** default XVCD)
b = mpeg1 vbr, buffer 224Kb (experimental)
2 = mpeg2 vbr
d = DVD
s = SVCD
v = VCD
-D v[,a[,a1]] sync correction for video,audio0,audio1 in ms
-c a-b multiplex selected time interval in seconds [all]
-B generates a profile template on stdout [off]
-F filename user profile filename [off]
-d verbosity verbosity mode [1]
-v print version
pat@anus ~/dvd/ $ tcmplex -m d -o temp/vts04.mpg -i temp/vts04.m2v -p temp/vts04.ac3

INFO: using reference profile (DVD)
INFO: profile type is (PAL)

INFO:
INFO: Scanning video stream for a sequence header and pulldown type ...
INFO: 2:3 pulldown detected ...
INFO:
INFO: Scanning video stream for pictures ...
*** Scanning video stream: 99% - byte offset 804115423 of 812237793. (99)%
INFO: Found 23411 picture headers, stream bit offset 6497789056.
INFO: Video stream information
INFO: Stream length : 812223632
INFO: Total time (seconds) : 976
INFO: Sequence start : 1992
INFO: Sequence end : 0
INFO: No. Pictures : 23411
INFO: No. Groups : 1992
INFO: No. I Frames : 1992 avg. size 71976 bytes
INFO: No. P Frames : 5853 avg. size 48509 bytes
INFO: No. B Frames : 15566 avg. size 24728 bytes
INFO: No. D Frames : 0 avg. size 0 bytes
INFO: Horizontal size : 720
INFO: Vertical size : 480
INFO: Aspect ratio : 0.7031
INFO: Picture rate : 29.970 frames/sec, 2:3 pulldown detected
INFO: Bit rate : 1225000 bytes/sec (9800000 bits/sec)
INFO: Computed avg rate : 1040000 bytes/sec (8320000 bits/sec)
INFO: Computed max rate : 1058300 bytes/sec (8466400 bits/sec)
INFO: Vbv buffer size : 229376 bytes
INFO: CSPF : 0
INFO:
INFO: Scanning audio stream for access units information
*** Scanning audio stream: 99% - byte offset 54124677 of 54669888. (99)%
INFO: Found 30508 audio frame headers, stream bit offset 437359104.
INFO: AC3 audio stream information
INFO: Stream length : 54669888
INFO: Syncwords : 30508
INFO: Frames : 30508 size 1792 bytes
INFO: Bit rate : 57344 bytes/sec (448 kbit/sec)
INFO: Frequency : 48.0 kHz
INFO:
INFO: Multiplexing information
INFO: Video stream data rate : 1058300 bytes/sec (8466400 bits/sec)
INFO: Audio stream 1 data rate : 57344 bytes/sec (458752 bits/sec)
INFO: Total data rate : 1260000 bytes/sec (10080000 bits/sec)
INFO:
INFO: Multiplexing file temp/vts04.mpg
*** Multiplexing: 99% - 53380 of 53919 A/V units. (99)%
INFO: Finished multiplexing temp/vts04.mpg
*** Multiplexing: 100% - 53919 of 53919 A/V units. (100)%

pat@anus ~/dvd/ $

I had this trouble too for a while; if I understand your problem correctly, the splitting of the first vob works fine, but the split data of the later vobs is unrecognizable for what it is by mplex (and a little bit weird as various players go. I had this unrecognizable output with both m2v and the ac3 data using tcextract.
What you need to do first is cat all of the VTS_1_0.VOB ... VTS_1_1.VOB.... into one big VOB. See, the problem is that ISO standard limits the size of any file, so VTS_1_[1-n] is actually all one vob, with crucial info residing in VTS_1_1.VOB (you can always lop off the #0 vob, I've found). Once you do that, you can split out the ac3 and m2v data from your vobwad, shrink the video as needed, and multiplex them back together. I found many sites talking about the extraction, but only one actually suggested the combining of all vobs into one lump vob. Weird.

ln -s /mirroreddvd/ERFMOVIE/VIDEO_TS/VTS_1*.VOB ./
rm ./VTS_1_0.VOB
cat *.VOB > moviewad.vob

Then play with the moviewad.vob

blah blah blah. Hope this helps, I'm too drunk to elaborate or care.