I'm having the same problem with version 1.2 installed with
some 'generic' mp4 video with ac3 audio in avi.
Playback in QuickTime (and Finder's Preview) is only 5 seconds and looks like this (audio is alright):

QuickTime Inspector incorrectly reports the following:
Notice that QuickTime incorrectly reports the data size as 2.14 MB and the duration as 5.12 seconds (the aspect ratio size was manually adjusted for posting convenience). MPEG Streamclip plays the files completely and without a problem and gives the correct file information:
The workaround:Using MPEG Streamclip version 1.9.3b2 and 'Saving As' an avi corrects the problem, allowing QuickTime to play the videos normally. 'Saving As' avi does not transcode/re-encode the audio or video, but (I think) simply re-wraps the mp4 and ac3 in a new avi container, thus fixing the problem.
I don't know if that helps anyone or if it says anything about where or what the problem is, but QuickTime is able to playback the videos correctly after doing the above workaround. I suspect that this indicates a problem with the avi wrapper and not Perian.
Edit:Seems to only occur when the audio is ac3, stereo or multi-track.