I was having problems with a/v desync until I started doing a double fix on the trimmed & demuxed AC3. What I mean by that is after I use VDMod to demux the commercial free AC3, I use AC3Fix.exe to "fix" the cut points. After that I run the fixed AC3 through BeSliced which typically fixes another one or two points. I used to just use BeSliced, but it wasn't uncommon for the AC3 to drift a bit. AC3Fix doesn't suffer this but it seems to leave errors in the stream (at least according to BeSliced). I haven't had a problem with sync since.
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