I recently had this same issue when I ripped these DVD's. My fix involved using VirtualDub to delay the audio. For the second discs on Two Towers and Return of the King (Fellowship didn't need it for some reason), I used the interleaving option under audio and punched in 500ms and let it run (direct stream copy under video) and when I attached the two files (also using VirtualDub) it came out perfectly. Easy fix, IMO.
EDIT: I originally ripped all movie files with DVD Shrink, and converted them using AGK, in case that makes any difference to anyone