That's really strange... no matter how my bay doors are locked, I can lock or unlock any one manually with the right key.  
You're sure, Dale, that you're trying the correct black-topped Key, cuz our '06 Monterey has two different ones that look virtually alike but have different applications.  Then there are two others without black tops that look alike.  To tell which of them went where, early on I put a yellow caplet on the engine compartment key (as in CAT paint), an orange one on the entry door latch key, and a green (like diesel nozzles) caplet on the fuel door key.  The bay door key I left plain.
We've experienced a number of issues when the keyless entry gets wet such as via rain.  And I've seen the thing light up and the lock activate on its own while washing the coach  

.  Eventually I had BCS richly seal the pad into its escutcheon and ditto the escutcheon onto the coach wall.  I examine that interface regularly and will smear Lexel if I spot a nano-crack.  It stopped the problem.  Otherwise even the slightest moisture seepage seemed to play havoc with the keypad.
As to Steve's suggestion, our coach that's similar to yours has door locks relay #20, 4th row of relays down and middle relay of five.  The circuit breaker is #CB17, 4th one down on the far left column (buss bar).
Joel