Audio sync issues in ClipWrap are almost exclusively due to issues with joined / spanned files.
Most AVCHD and HDV cameras split recordings into 2 or 4 gigabyte chunks called spans. In order to properly play these chunks, they need to be reassembled before converting them to another format. If they're not reassembled properly, audio sync can slip due to the way cameras make these splits.
The "join" functionality in ClipWrap can handle this for you. By adding the root "PRIVATE" folder from an AVCHD card, ClipWrap can automatically reconstruct spanned clips. Alternatively, you can manually join files using the clip menu. See the manual for full details.
Sync can also slip if you try to join files that weren't originally split by the camera. If you just want to combine a variety of shots together, we recommend that you do that after converting or rewrapping your video. We recommend the AddMovie application for this task.