Outlaw,
I had this same problem with a few of my movies and it drove me crazy for a solution. The easiest way to tell if this will happen is to open up Windows Media Encoder (WME), as described above, and go to 'Properties' 'Sources' and check out 'Mark In/Out'. If the duration doesn't look right then you'll have a problem.
To fix this, just use DVD Decrypter in IFO mode. Go to the 'Stream Processing' tab and choose the video and which ever audio you want. Just make sure to have the 'Demux' selected at the bottom. After you decrypt, the only files you'll need are the: *.m2v and *.ac3.
Now when you open up WME, just make sure to give it the seperate video and audio files for the 'Source 1'.
Hope this helps,
Golgo
Also, I found a way to include the sub-titles for foreign movies and forced-subs for english movies with the occasional sub-title in it. But it does add: 1 more program, 2-3 more hours, and quite a bit more input from the user. Let me know.
** update **
The Demux step I mentioned earlier seems to be causing an audio/video sync problem in some movies. The beginning is fine, but by the end of a 2 hour movie there could be as much as a 5 second difference. This is fixable but adds alot more steps and more software. In the end, it's just way too much trouble.
Now I just end up going the DVD to MPEG/AVI to WMV route. This makes the whole conversion process about 2.5 times the length of the movie. It may take a little longer, but it you'll save in head-aches. It's a much more consistant process. Just be sure to check the 'Mark In/Out' time in WME first.
I'm now using
DVDx 2.2 for the MPEG/AVI encoding. This will also burn in subtitles for movies that need them.