I've tried Virtualdub, Virtualdubmod, Virtualdub mp3 freeze to scan for bad frames in my selected files and I get the "NO BAD FRAMES FOUND"
message.

But I know there are bad frames, (causing my audio to go out of synch)
because using any Virtualdub, I can see them when I manually advance the file I have opened frame by frame, or even keyframe by keyframe.
When I come across the bad frame(s), Virtual dub does display a note at the bottom of it's window telling of the error.
The bad frames have a pixelation or are frozen for a few seconds.
I know how to remove/mask them, what I'd like to know is how to scan for them more sensitively.
I can do this manually with absolute certainty that I can locate and remove all bad frames, but have you ever tried manually scanning a movie one frame at a time?

Help is appreciated.

Heres an option http://divxrepair.sourceforge.net/

not sure how sensitive this is since you said that virtual dub is able to play past the corrupt frames but it is worth a try.

Tried it, didn't work. It reported no bad frames, but bad frames are still there.

Maybe the frames aren't "bad" enough to be detected by any of the Virtualdubs, but bad enough to throw off the TMPEGEnc audio/video synch.

My only option is still to go through the file manually, frame by frame.

Is there a setting option in Virtualdub to increase it's sensitivity to any amount of data corruption?

I dont know of a way to increase the sensitivity unfortunately.

Are you sure it is bad frames that is causeing the sync issue and not framerate or audio frequency (44khz or 48khz)?

Framerate is not a problem. (I know it's an issue that's been raised by some, but not in this case).
Audio is something I've had a pretty good mastery of from early on, so it's not that either.

I can actually see the "bad" frames in any Virtualdub if I advance the clip
one frame at a time. It will then come across a corrupt frame, and I can visually see pixelation or other distortion.

Is there a way to get TMPEGEnc (my encoder of choice) to not be so picky about bad data?

Its a long shot but if you are using 2.510 you could try a previous version, I have found 2.58 and 2.53 work better with slightly suspect sources but I have never had audio synch problems at all.

Good suggestion. I'll try it and let you know.