I have a similar issue. My Vista PC is a Asus CS5110 Essentio which comes with a remote for Media Centre.
I recently applied SP1 and other available updates around the same time my remote stopped working. The remote will only work to turn the PC on. once the OS loads, the remote has no functionality. This suggests the remote itself is ok and that the issue is a software problem (drivers
Device manager seems fine. And the HID services are running.
I'm going to try rolling back to a restore point before each update I applied and see how I go...
Anyone else have any ideas?