I have the same problem. My cougar MFD's use joystick ID 1 and 2. My G940, 3,4 and 5. When I save a profile and load it again, the keyboard mappings are removed and replaced with the joystick mappings (ID3). And both cougar MFD's (ID1 and ID2) are mapped according ID4 and ID5. So all the mappings are moved to the left.
Also after editing the profile for about 15min the program crashes when clicking on the description on the left. I had to do it three times to finally got it right. Tip: pressing OK frequently and start options again also saves the mappings.