This subject has been discussed in the AnyDVD boards and it seems I was configuring both AnyDVD/DVDFab in the wrong way, regarding the region-code (also read the part where I told my LG drive was using factory settings, no region set):
Aditional steps required to decrypt some DVDs - SlySoft Forum
Once I get my hands on the quoted discs (Harry/SF) again, I will test if something changes. So perhaps the navigation issues experienced by some players were a result of those wrong settings, and perhaps the "region marking" error from the "When Harry Met Sally" disc was solved with those steps... perhaps PGCEdit wasn't necessary at first, after all.