I don't know if this will help but I have had a similar prob. with video mpg2, video not syncing with audio. Following some great advice from Tsantee, the orig encoded mpg2 had audio at 44khz, Toast recognizing only 48 khz. Toast will burn file but will not be able to sync up the audio when it muxes the file. The orig file needed to be resampled, in my case I used Mpeg Stream clip by Squared 5 (free) and apple's mpeg playback component. Exported the file as a DV file, with a resample to 48 khz....toast burns new dv file, and now the video syncs up with the audio. Note that here, in my case, Toast encoded the file instead of multiplexing of which I have set to 'never encode'.
It may sound like apples to oranges but its a similar concept and may offer a new path to help you find some software so resample the audio. (Maybe? I hope, since I understand your frustrations, it took me two weeks to resolve my issue) Check out the discussion thread in Forum Toast 7, "My TV.PVR and Audio" that may offer some kind of spark or added insight.
also I have never heard of the file that you are describing but maybe Mpeg Streamclip can help?
(I hope I added the above link alright, bear in mind I am a Newbie!)
eek wrong url....dropped the 'l' ... here it is!
Squared 5, Mpeg Streamclip