Thanks for the reply, it is much appreciated.
The Cancnc forum was helpful, and it got me through initial set up issues, however, the latest problems don’t seem like easy fixes.
I tried all sorts of configurations on the motors (pins and outputs) but nothing seems to change the problem.
The strange thing is that each time I start up, the problem seems slightly different. On one start up everything worked fine, but without changing anything, the very next start up, had the gantry making a graunching sound, and randomly jiggling around.
I am going to try disconnecting all the interface cables and check for pin problems etc. The MP3000e box looks pretty battered about.

Thanks again.