I have read through other threads regarding an issue with MJPEG (MSI Codec, .avi format) and Premiere. I was doing a Bioshock game commentary and everything recorded well. I loaded it into Premiere and it also played well there. I waited for the audio to conform and everything played well and was synced properly. It wasn't until I split the 1 hour gameplay into 4 segments and exported them that the audio goes out of sync. From what I can tell, while I'm on the games main menu and talking, all is well. When I start the game up, somewhere in there it adds a 6 second audio delay.
I also tried to convert the .avi file to .mp4, but when I do, there is also a 6 second delay in the .mp4 file. I have installed the Morgan MJPEG codec v3.
After trying a bunch of options, this was the best:
"Another option: get MPEG Streamclip. It's free and no installation is required. Try opening the file there (it should open). If it does, go to File > Save As, and save the file as an MOV. You can leave the file name the same. This will rewrap the video in an MOV container without any transcoding and no quality loss. The rewrap should be pretty much instantaneous. Try importing that into Premiere. If it works, and you have a bunch of these, you can set up a batch rewrap by going to List > Batch List and adding all the files that way."
I then imported the .mov into premiere and everything was great. It may not be a definite solution, but was a pretty good work around!