Maybe you forgot to solder the jumper for the 5v on infinikey board. Which revision is your B board?
It could also the B board doesn't sit properly on A board.
@nem Do you know how to program IR Codes with Remote Master software? I went through the hifi-remote.com site and tried to program my JP-1 remote (ARRX15G) but I got lost. I also posted at the forum of that site asking for help.
Which button do you press to turn off the overlay? This page listed the code for each of buttons.
https://gamesx.com/wiki/doku.php?id=x68000:go555sa_monitor_remote
I have never programmed a remote. Any idea where to find info about it?