Ok. I have tracked down the issue here. My A1200 is set to one of the screen modes BetterWB provides "PAL High Res Laced 640x530" with 256 colours. If I set the colours to less to 32 (anything less than 64 actually) then the game runs perfectly.
I just tried this with a vanilla Workbench 3.1 with various screen modes and colours and these all worked fine.
So at a guess I'd say this might be something to do with how Scorpion sets the screen mode and palette and that seemingly does not play nicely some of what BetterWB provides.
Hopefully this is useful for some folks.