I am using version 4.08 and have the same problem. Everything is great in Editor and Preview. Once I export, it is out of sync. This only occurs when I edit the video and make a new sequence. During the transition it looks and sounds perfect in editor, when I export, the transition points are off by several seconds. I had Custom settings of the Preset file setting.
File Format: .avi
Resolution: 1920 x 1080 - YouTube 1080p
Maximum Frame Rate: 60.00
However, if I Export as a Video File and select DETECT Preset, it changes to MFR 30.00 Then it seems to be ok.