From the software side of things, everything looks ok then and your Apple Remote should work correctly. Since you already exchanged the remote's battery, that shouldn't be the issue either.

On the hardware side, these could be possible causes:

1) the remote itself might be broken 
In that case, even exchanging the battery wouldn't help. If you have a webcam attached to your Mac, you can check whether your Apple Remote sends anything using Remote Control Diagnostics' Battery Check.

2) the receiver itself could be broken - or might not have been seated correctly when the Mac mini was reassembled after repair 
I can only guess here, of course, but if I understood you correctly, the Apple Remote has not worked once since the repair, so this is something to consider.

Best regards, 
Felix Schwarz