Couple of things to look at:
1. What version of TOS do you have in the STFM? TOS 1.04 is the best version to use when you have mass storage devices.
2. Have you tried a warm reset? It takes a bit of time for the Pi to boot its OS completely and you may just find your ST’s cold boot completes just a little too fast. Try booting up, then reset the machine rather than power cycle it.
Mega"SST" 12, MegaSTE, STE: Desktopper case, IDE interface, UltraSatan (8GB + 512Mb) + HXC floppy emulator. Plus some STE's/STFM's