We are getting a number of calls on audio sync issues with MegaPEG.X and the MegaPEG.X QuickTime plug-in.
If you have problems with Audio sync and you are using a version of QuickTime previous to version 7.0.x, then the audio sync problem probably is related to a bug in MegaPEG. The workaround is to encode using custom settings, and then bring up the System tab and make sure the 'Audio Sync Offset' slider of the multiplex is set to 0 ('zero'). This setting should always be zero unless you have a special application.
If you are using MegaPEG.X 2.x and QuickTime 7.0.x, then the audio sync problem is related to incompatibilities with our 2.x version and QT7. Upgrade (free) to the latest MegaPEG.X 3.x and the latest QuickTime version.
If you have continuing troubles, please contact support.