@amiga1260:
Your problem is in 3.1, not in 3.9. 3.9 does it correctly. Your 3.1 setup is very dangerous, you will loose all data sooner or later because your partitions share the same storage. The Work partition will destroy all the other partitions when it fills up and vice versa.
Please run Check4GB from Aminet. Run it once on 3.1 and once on 3.9 and post both outputs here.
To repair your issues, you should copy all data from the work partition to one of the other partitions, then run OS 3.9 (remove the skipromupdate first !), make sure that FFS V43 is installed in the RDB, format the Work partition and copy the data back.
With FFS V44 (a.k.a. FFSTD64) you don't need to do anything else, with FFS V43 (old beta version) or V45 (comes with OS 3.9) you need to install NSDPatch to the 3.1 partition. Or better extract scsi.device from the OS 3.9 ROM update and activate it with LoadModule. NSDPatch is crap.