Ok, this is very strange. I found that disabling a bunch of checkboxes on the SYSTEM page caused the remaining faults to disappear and the project runs properly.
Narrowing them down, it appears that enabling either 'prefetch mode' or 'cycle accurate mode' (or both) will break my project. The other checkboxes don't seem to contribute to the problem.
The main difference between this project and BadMooD is use of the FPU, mainly within C code. I didn't see these issues with BadMooD.
Not sure if that helps make sense of whats going on.
D