I may have the answer but best to check in case my PC has a weird fault. I have lost all of the keyboard assignments and the control profile has reverted back to default. The only thing I did was create a new pilot and delete the default one so am I right in thinking that the keyboard assignment profile is somehow attached to each pilot in the Pilot menu roster?
EDIT: Just did a quick test and it appears the profile is assigned to a particular pilot and, if the pilot is deleted, aargh - so is the profile.