When I installed AutoFLAC, I gave it the locations of the 1.1.4 versions of flac.exe and metaflac.exe. When running AutoFLAC/EAC, everything seemed to work properly, except the wav files were not converted to flac files. When I gave AutoFLAC the location of the flac.exe and metaflac.exe files that came with AutoFLAC, it worked fine.
Thanks for the great script!