I just downloaded the RotJ .wav file and was having the same trouble as with the ESB file. I used the flac program again and sure enough it fixed the problem just like I said in the previous post. This time I took a screen shot of the DOS box from within which the flac program runs, so I could type up any error messages that might help us to figure out what's wrong with the original .wav files. Below are the error messages that showed up in the DOS box while the file was being compressed from the original .wav file posted by boba feta and put into a flac file.

ROTJ '93 DVD.wav: WARNING: skipping unknown sub-chunk 'bext'
ROTJ '93 DVD.wav: WARNING: skipping unknown sub-chunk 'minf'
ROTJ '93 DVD.wav: WARNING: skipping unknown sub-chunk 'elmo'
ROTJ '93 DVD.wav: 100% complete, ratio=0.443ROTJ '93 DVD.wav: WARNING: skipping unknown sub-chunk 'regn'
ROTJ '93 DVD.wav: WARNING: skipping unknown sub-chunk 'ovwf'
ROTJ '93 DVD.wav: WARNING: skipping unknown sub-chunk 'umid'
ROTJ '93 DVD.wav: Verify OK, wrote 672631682 bytes, ratio=0.443

Tag - Automatic Tag from filename

C:\ROTJ '93 DVD.flac

Tag guessing failed.
Format: FLAC
Details 48000 Hz Stereo, 137 kbps, playtime 02:11:41

And then several lines below that it said something like " General Error: 1 "

Do any of you audio experts recognize what these error messages mean and why they happened?

And do any of them have any chance of meaning that the .wav file after being compressed by this flac program, and having these error messages come up, and then uncompressed back into a .wav file will no longer be perfectly synched to the ESB and RotJ video for some reason?