i also had issues with SFS, FFS, PFS regarding long filenames.
now i finally put the latest and freeware (?) version of PFS on my A1200 with a <4GB HDD.
i partitioned, updated etc. and formatted the disk as described in the guide.
AND !IMPORTANT! set the filelength to 107 for every partition.
no problems since then again with long filenames!
everything's fine now, DOpus 4.12 can't handle the long filenames, as it could in FFS/SFS (but SFS sometimes failed) so i have to use DiskMaster2 now for fiddling around with files. :-/