I ran into a few audio sync problems with Womble when I tried editing the Lord of the Rings films. As Marvolo mentioned, the Womble MPEG Video Wizard DVD (which has a 1 month free trial available on the website) spits out DVD files free of sync errors. However, putting the output video & audio files through a DVD authoring program resulted in errors. One way of getting around this (though it may degrade the quality of the audio) is to import the output video & audio files back into Womble, zooming in to the end, and noting the number of frames the audio was off by and also calculating the # of seconds of both the video and audio. Then, I brought the audio file into a separate program (GoldWave, btw), noted the running time it reported (for some reason, it was usually different from the length Womble stated), and worked out a ratio to find the number of seconds the audio should be according to GoldWave. Then, I used the time warp feature to get it to the right length. I then brought the new wav file back into Womble and it synced up brilliantly. Of course, this method probably degrades the original audio and so it may not be an option for some.

As far as audio hiccups went, I would try encoding it several different times, each time maybe overlapping audio clips more and more and fading them into one another until audio pops disappeared. Still, most of my methods seem like cheats. But it works for me since I'm not an audiophile.