Great! I will add that to the emulator documentation on the site, I wasn’t aware that it didn’t auto-associate .fs-uae files to FS-UAE on Windows, it does that

Great! I will add that to the emulator documentation on the site, I wasn’t aware that it didn’t auto-associate .fs-uae files to FS-UAE on Windows, it does that without any user interaction on Mac. Can’t do much about emulator bugs, those need to be filed in the respective issue trackers — could be a WHDLoad problem too. As far as I remember it runs fine on the MiSTer FPGA, but I should double check.