Hmm not sure if this will help, but this is the commandline I use with mencoder to rip DVDs with no audio desync problems. Maybe if you use much the same, but change the input from DVD to a file (or files) it might help?
Code:
mencoder dvd:// -o outfile.avi -oac mp3lame -lameopts vol=8 -ovc lavc -ffourcc DX50 -lavcopts
vcodec=mpeg4:aspect=1.78/1:vbitrate=1800:vrc_eq=tex:naq:ilme:trell:cbp:preme=1:keyint=132:mbd=1:qns=1:vme=4:dia=2 -noskip
try for the "dvd://" part
Code:
mencoder "mf://*.jpg"
with the rest of the command the same
For example, change "mf://*.jpg" to the filename you have
I'm reasonbly sure the above won't work (there's no info / command about a sound file, which you seem to have separately) but if you mix and match with your commandline you already have it might help?