If you purchased your Qio before November 2011, you will need to update internal Qio ROMs to allow Windows to enable hot plug. This updater needs to be run from a Macintosh.
The Qio BIOS software is not running and it must run to re-arrange the PCI busses. Because some PC's BIOS's do not allocate space for empty PCI slots, you may need to boot your PC with a card installed in one of the slots in the Qio. You can verify that the Qio BIOS software is loading by checking to see the Sonnet banner in the BIOS startup.