Have you tried following this:
Videora Conversion Guide:
http://www.videora.com/en-us/Converter/guides.html#2000
Also here is the Bug list for Videora from their web site. One pertains to your problem:
Known Bugs
Audio/Video sync
Problem - Output files can be out-of-sync. While no set pattern has been established, it seems to be more frequent with input files of 23.976 fps, non-DVD rips, and WMV/MPG filetypes.
Workaround solutions - Try the custom option '-async 1'. If the disconnect gradually increases over time, setting 29.97 fps sometimes gets rid of the problem regardless of the input fps. You can also use AviSynth to assume the FPS and have the audio sync to that. If it's a sudden disconnect, check your VOB Cell settings in DVD Decrypter settings per this thread. Otherwise, test with an AviSynth script per the DaProphecy's method in the FAQ. For non-DVD files, PSPVideo 9 may be a good short-term solution until the converter stabilizes some more or try something like AviDemux.
Audio track not getting picked up
Problem - The IFO stream rip is fine, but the converted file has no sound. The debug info showed to audio track getting picked up. The most obvious case with this is the Madagascar DVD.
Workaround solution ideas - Test with an AviSynth script per the DaProphecy's method in the FAQ (untested). Use a different DVD ripper.
Program doesn't start (.NET issue?)
Problem - Converter errors upon starting with an extended dump.
Solution ideas - Update .NET framework (in all languages you're using!) to most recent solution. Clean out registry. Neither of these have worked for some.
Progress meter incorrect
Problem - During transcodes, the progress meter can be incorrect; thus, transcoding continues after the meter hits 100% and time remaining is zero. People have been seeing this more often with VOB files and/or the H.264 codec.
Workaround - Figure out the length of your movie in seconds and compare that to the 'Processed' field. A 2-hour movie will not finish until Processed hits 7200 seconds.
Artifacts (bad video quality) in darker scenes
Problem - Scenes with darker background colors tend to have more artifacts (blocked video). It's much more obvious on the iPod, so this may be an Apple firmware problem.
Workaround ideas - Use a VBR setting (FQ->VBR, two-pass A->VBR) to improve video quality. The custom option '-mbd 2' might help.
Desktop icon
Problem - When installing, the desktop icon does not appear/stick when using lower color setups.
Workarounds - Select a 32-bit color scheme in your desktop settings, or change the icon in the shortcut.
Profile changes don't always stick
Problem - If you make a change to a profile, click apply, and immediately trancdoe with that profile, the transcode might not use the new settings.
Workarounds - Once you click apply, swtich to another profile and back again to make sure the change is still there. If that doesn't work, create a new profile.
Can only install/use with admin rights
Problem - There have been reports of non-admin users not being able to use the converter.
Workarounds - Separate installs or give all users admin rights.
When will known bugs get fixed? When will new features get added?
The textbook answer is "whenever they get fixed/added." My honest, direct answer is "I don't know." I am not officially associated with Videora or any of its employees. I only have mod rights because I asked for them in order to organize this forum a bit.
