Pics?
Note that BMS has the tendency to "reset" game controllers if they're not plugged in or turned on or configured the same way as you did the last time you plugged it in. To give you an example, I fly with a TM Warthog
HOTAS but my specific profile needs to have both stick and throttle "combined" so that BMS sees the WH as a single controller, not a separate stick and a separate throttle. If I don't "combine" my
HOTAS before BMS starts, BMS will reset all my axis settings and stuff.
The "fix" for this is to mark a couple of files as read-only, that way if I forget to "combine" my
HOTAS, BMS can't re-write over my saved settings.
So make sure that you connect the controllers to the same USB ports, maybe even connect in the same sequence.... or better yet, don't disconnect anything.
Also make sure that your controllers are properly configured (ie, if you need to load up a profile) before you start BMS.
As for the BMS Full.key file, maybe you could move the default .key files from the
\User\Config folder and just keep your own .key file there.
Just a few ideas...