Inverting audio ruins video

[Metrophage]

Major's advice on processing MJPEG .MOVs as MP4 worked perfectly for getting audio and video in sync. But it turns out that QuickTime exports these MP4 files with the audio stream first, so they need to be inverted.

Problem? When I wasn't inverting the streams, the video always encoded perfectly, but with no sound. Now when I invert the streams I get audio, but the video is encoded jerky, so it looks like it is 3 FPS or so, even when playing back full speed. I have tried many different encoding types, XVID, DIVX, MP4... FFMPEG and MENCODER. Same deal. I find this extremely frustrating, mostly because I don't understand how or why this would possibly be a problem. I can understand frame capture on a slow machine losing frames, but my machine wasn't breaking a sweat with the transcode, and it seems as if each frame would obviously be after the next.

Any chance that somebody might hopefully be able to tell me what is going on here? And/or how to fix this?

Thank you!
M

[Metrophage]

My first tries were with audio which was 44.1khz mono, so I have since then tried doing the initial VHS capture in 48khz stereo - hoping the problem might be some weird trouble with sample rate conversion. No dice! I have tried all of the Divx and XviD codecs and options and the resulting video has all the while been unwatchably choppy. The source files are fine.

Can somebody please tell me what is happening here? I have been encoding stuff for two weeks straight and my drives are filled with this stuff. I'd love to succeed in just making 700 MB XviD/MP3 files of these things, I don't understand what is so complicated about it. I tested a few DVD rips and those were a snap. Why the MJPEG/AIFF to MP4/AAC problems?

Thanks
M