Joypad no longer working with 1.3.1

I had been using my joypad fine until recently I upgraded to 1.3.1. The joypad still shows the correct 2 light mode and is connected but it will not operate the machine. Is there a setting I am missing in the new firmware to enable joy pad operation that I am missing?

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Have the same situation here. Joypad has the upper two blue lights showing, but unable to move machine with joypad.

Anyone have any ideas?