I know this has been an issue discussed in threads before, but I haven't seen any commentary to put this issue to rest once and for all.
Using TMPGEnc 4 Xpress, I routinely transcode music videos from various sources to mp4 for use with AppleTV. The end result is always an audio skew of approximately -135ms (audio too early). Quicktime will play it this way, and with iTunes and AppleTV it is even more noticeable, but other applications don't seem to show much of a sync problem.
So, in order to correct this, I have to process each clip with a correction of +135ms so it will play right in iTunes, AppleTV, and QuickTime players.

Not knowing this was an issue, I created a library of over 300 videos with sync problems, and have spent months recompiling the original material and preparing it to be reencoded with the proper correction.

What I really want to know now is, WHY does this happen? Is the codec poorly written? Is it merely the way it interacts with the software I use, or is it a configuration problem that I'm just to ignorant to pick up on?