I am having this same problem with my video files and CS5. The files began as .avi files, but there was no audio at all when imported into Premiere (Xvid codec, apparently a known problem), so I converted to .mp4 and now the audio un-syncs from the video over time. The specs for the converted (mp4s) are:
Video: (avc1) H.264/MPEG-4 AVC
Audio: mp4a: MPEG-4 AAC LC
Very annoying. Video is in sync with audio at the beginning but slowly loses sync over time. Not only is it out of sync within the program but also when rendered. The original file is fine when played on VLC. Will look to convert to .mov I suppose. It's difficult (from my naive perspective) to understand why importing videos (having seemingly popular codecs settings) is so difficult. Are there any other work arounds that are known for avoiding this? I don't have QT Pro and would prefer to avoid spending another $30 just to convert. Or is there a freeware .mov converter that is known/popular?