afrer some testing i had to switch back to PIO 4 because with pio mode 5 even if drivetest report "OK,no errors" i have a lot of checksum errors and locks.. with PIO 4 all appear to be ok. one little difference is that my A4000 mount a fastata mkvi with rom 7.0 (but i do not think that's the problem) have you tried to remove setpatch command? just for try, or another version of setpatch/fastata.driver
i've a lot of sh*it that loads on my amiga 4000: mmu, mui, poseidon, cybervision, modified cyberstorm libraries.. when i've some free time i will try to unload all, and put another hdd with clean workbench install and only fastata driver (ofcourse stock cyberstorm libraries from install floppy) i would try os3.9 too