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My research is definitely a bit data (using one of the first Intel mac minis), but my findings were the same: I couldn't get Windows to see the IR Sensor.  The Apple remote worked for a few commands, but not all, and I couldn't use the IR receiver with a different remote.  Definitely some type of weird filtering they are doing for the IR receiver.  I think you're out of luck.

It's like they don't want you able to really use Windows on a Mac....

Milhouse