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Just started playing with that as I read your reply
I'm no pro when it comes to dvd copying etc, but I can only assume that ripping a DVD to an ISO, then using gnomebaker/k3b to burn that ISO to a DVD "should" theoritically be an identical copy of the original, therefore it will play on any dvd player?
I've tried using various windows tools to rip/burn DVDs but it seems the formatting gets corrupt :S
You might try DVD95. I just pulled it in from synaptic on my Ubuntu machine (7.10) and it looks like it does pretty much what the windows program DVDShrink does, and it looks like in the prefs you can set it to, instead of shrinking a dual layer down to a single, just copy the dual layer.
If that doesn't work (and I confess I haven't tried DVD95 before) then you might try installing DVDDecrypter or ImgBurn (preferably the latter) in wine. They both work flawlessly provided that you configure your wine environment for them as NT 4.0 and ensure that wine is detecting your CDRom correctly (I think by default it doesn't, perhaps just in ubuntu, though I think I had to check that in slackware too not long ago).
You can't just burn the video_ts and audio_ts to a disc, I think the file system has to be just so (UDF I believe, and the disc has to have a name in the correct format, and so on) and perhaps some other magic has to occur for a standalone player to recognize the disc. To play a disc from your hard disc, I think you can just drag the video_ts folder directly onto vlc and it will play as if it were a real disc. To burn it, you can use k3b, I believe choose video DVD from the new prjoect menu (k3b isn't installed on the computer just in front of me, but the option is there in the k3b menu someplace). You can also use the windows program ImgBurn to build a good ISO from the video_ts folder, even if you can't get it to recognize your optical drive under wine.
The -dvd-video flag tells the program to write an iso that can be played in most dvd players.
The -V flag is for the "volume label", you can think of it as a name.
The -v flag is for "verbatim" [and of course you can omit it].
The -o flag stands for "output"
Finally dir_with_dvd_structure is the directory that contains the directories VIDEO_TS and AUDIO_TS.
Hope this helps.
If using a terminal is not an option you can install "devede" from the repos and produce an iso file from a dvd structure.