Didn't see all your first reply a cf adapter can be fussy and I have seen where you have to set them a master and your hd as slave, how big is your cf card?
Do you have a SBC card with a backplane?
I have also had to use different brand CF cards on occasion.
you should be able to put your newer control in the spare box worst case scenario would be getting acroloop.hex files from Milltronics if the ones from the older control do not work correctly with the CSM setup.
They only charged me $100 the same as they want if you request a parameter backup file to be emailed to you IF they have it on file.