@ CU_AMiGA:
Check to make sure the computer is actually soft booting the OS 3.9 ROM image.
If not, then it will not be able to correctly access partitions on big disks.
An easy way to tell is type "version" in a CLI, you should get something like this:
Kickstart 45.57, Workbench 45.3
Kickstart 45.xx is OS 3.5/3.9 in ROM.
If you get 40.xx it means you are running OS 3.1 only.
If this is the case, check the Setpatch entry in the startup-sequence.
Also, I'd recommend using PFS3 as a filing system. Had it for years and have never had invalid disk problems. Plus it lets you use disks as big as 2Tb!
