I’m affected by Bug #48773, which, if I understand it correctly, means that my Nforce2 motherboard’s BIOS (the latest, FN45S00W from Shuttle) doesn’t treat the shutdown signal like it should, leaving all USB devices powered on. Windows (XP) isn’t affected or maybe it has a workaround – possibly something similar to the one presented over at Launchpad and Kernel Bug Tracker.
My setup doesn’t have annoyingly bright lights, but I do have one particularly troublesome issue related to this problem: my USB keyboard doesn’t seem to be able to wake up when I turn the power back on. I have to unplug and replug it in order to resurrect it. There is a weird performace issue in Windows when I hook it up into the PS2 port with an adapter, so I’d rather keep it plugged in as a USB device. But I may have to reconsider, since an official fix for the issue is considered unlikely.