Okay, well Microsoft is breaking more and more of Windows, particularly the consumer stuff like IR, so it could be just another example of that.
But the PC is locked, and it happens after a while, is outside MC... Antivirus. With a locked PC most AV will start to do its background stuff after a while. If it detects "keyboard" activity while locked it may deem that to be suspicious, and so block it. A reboot fixes the issue because the AV isn't permanently blocking the service.
The other possibility is power to the device is being reduced, or as this is a USB device it is being "Suspended". In that state, it may still be able to draw power for the hardware to run, but the data communications are effectively turned off. Hence the lights still work on the receiver as they are purely a local hardware feature, but nothing is received by the PC.