I've had a couple of videos today, for absolutely no reason, not sync properly after exporting.
Both were originally in mp4 and play totally fine in Windows Media Player and VLC. No skipping, no nothing. All I did was import into Premiere Pro to add a watermark and then export as H.264
After exporting when I play back, the first half is not in sync at all, the other half is totally fine. It did the same to another video where it kept coming up with an red box at the bottom right about a frame error. In the preview window it is fine so it's super annoying.
Exactly what is INSIDE the video you are editing? Report back with the codec details of your file, use the program below Free program to get file information for PC/Mac http://mediaarea.net/en/MediaInfo/Download - when you analyze your file in MediaInfo and post a screen shot in the forum, do so in TREE view