I'm using latest beta release.
I've had this issue since day one.
I just re-installed Windows 7, same problem. Nothing installed on it but XBMC.
The remote works great for my TV and Denon amp (powers them up, volume control etc) just that 1 minute lag on Flirc that I need to get close to it for it to receive the commands from the remote.
I've set the computer to not power down anything (display, harddrives etc etc) it's in high performance mode basically.
Maybe now that I'm thinking about it, could the USB have some sort of power saving mode? I'll have to go through the windows settings some more.
Hmmm ok I found a power saving mode for USB in device manager and it was enabled.
I disabled it and see if that will fix my issue, I'll try it after a few hours of it idling and again in the morning.
I'll keep you posted.