I’ve had the same issue on a few occasions in the past. If you are exporting a comp that has audio sync exactly like you like within AE, chances are it’s being exported properly. Try exporting 1/4 resolution, a lower bitrate audio and a compressed codec like mpeg2. The resulting media should be very small. When you play this back, it should be easy for the workstation to play this media file. You should have sync. If the sync goes awry when you export in your chosen codec combination, it’s simply a decompression issue in your media player. I’ve never had an issue where After Effects exported out of sync. It always turned into a problem with my media player trying to play the file as exported. Must have been too big, or too high bitrate, etc.
You can also try to export normally, import that file into FCP or Premier, then render out into DVD or .mov. That will probably have sync as expected, proving that your original media was fine.
As a last bit of troubleshooting, something I’ve had to do on occasion is put in a frame-counter effect bottom frame. Find a few spots on the timeline that audio peaks or something of note happens. mark the frame number/timecode displayed. Insert a few frames of 12dB tone or something notable at that moment on the audio track. Then export. Goto that frame on the exported movie, and click play. Should hear the beep when you hit play, which means the audio is exactly in sync, but wanders off when playing.
CS3 – Mac
C4D