[Abra Cadabra IV]

Nothing quite like what you're describing popped up at Vegas this weekend, but several similar FMS issues did. (We had the reverse happen to us; our button-controlled servos would randomly not respond near the end of the day, but we suspect a short in our servo cable rather than any field problems.)

I don't know exactly what causes these errors, but my team discovered that keeping the batteries fully charged and power-cycling the NXT between matches keeps weird control issues to a minimum. Also, are you positive it was the FMS? Do you have things that were hooked up to both joysticks and buttons, and that would only respond to the buttons in those cases? If not, I'd check your wires and motor/servo controllers.