Can you try starting EmuTOS directly, e.g., by passing the ROM as
commandline argument "--tos etos512uk.img"?
That thought occured to me as well but even when I saved the setup with EmuTOS as ROM, i.e. immediately starting EmuTOS after Hatari's launch, it didn't change a thing.
However now that I see that it behaves the same way on Linux, I could rule out multiple things and found out that... I still don't know whose bug is it. ;-) The crucial difference between a working and non-working scenario is whether I supply "." at the end of Hatari's command line.
If I take my Windows cfg file, open it in a Linux editor, change szHardDiskDirectory to my home folder, exit and "cd /home/mikro":
- hatari -c hatari.cfg and choosing EmuTOS and reboot shows the bug
- hatari -c hatari.cfg . and choosing EmuTOS and reboot doesn't show the bug