My problem with long file names was definitely present in PFS 3 & PFS 2, and probably before then as well. It definitely occured under OS3.9.2 with Amithlon (with SCSI disks) & WinUAE (with direct access to IDE disks), and probably on my Blizzard PPC A1200 too.
The easiest way to cause the problem was to get AmiNetRadio to make some recordings to disk, which creates MP3s typically with ridiculously long filenames (depending on radio station). Unless I did it to RAM disk there would frequently be problems.