I've just successfully flashed my Gemini, but to get it to get the FlashTool to recognise the Gemini I had to disable memory protection in Windows 11:
Windows Security > Device Security > Core Isolation
After a Windows reboot the Gemini could be flashed. Just reporting here in case anyone else has the same problem in future.
To turn on Core Isolation again afterwards I had to remove the FlashTool drivers (slightly technical, but a quick google solved the issue)