At Rf bad connections can act as diodes, something that could could have happened, do you have a cap across the power rails on the board, a 10u and 0.1u in parallel is a must for something like this, battery impedance tends to rise as they discharge and weird stuff happens, the cap keeps it down.
Might also be worth trying a couple of diffrent batteries.
I had a tv infra red remote that would only work on a bench psu, , it was an open electrolytic across the supply.