Do you lock the doors with the remote everytime you leave the vehicle? Because if you don't, it may confuse the car as to which settings to recall. Think of it this way:

Lock = save previous settings.
Unlock = load previous settings.

Whenever my dad confuses the car, I simply go back with both keys and resave the memorised settings. Unlock with Key 1, push seat memory M1, lock. Unlock with Key 2, push M3, lock. Then I unlock with Key 1, and it goes back to M1.