Pat/Mark,
This sounds like a date/time stamp issue with the files in the RealTracks folder ON THE AUDIOPHILE VERSION ONLY, and should be solved from a patch, which Andrew @PGMusic can get to you (online). LIkely something in the copying process changed some file/date stamps.
Could you please check out a sample folder, and tell me if the date/timestamps are all the same - ie) the bt0/ WAV / WMA have the exact same date stamp.
For example, for the folder "c:\bb\Realtracks\Bass, Acoustic, Bluegrass Ev 130" do all files have the same date/time stamp?