5. Look in the BIOS to see what the USB support settings are. Try changing them to see if it makes a difference.
6. Check the MoBo manufacturer for a BIOS update
Good luck! :)
Go into Control Panel > Power Options and select the "Always On" power scheme, and see if that makes a difference. You might also have power management options to turn off in the BIOS. What I am suggesting is to turn off all power saving options such that only you should be able to turn off the computer. If that does not temporarily resolve the problem then I would say that it is probably not power management based, although it could be your USB management software.
It is interesting that the iPod doesn't provoke the problem............could that be because it has an independent power supply? Can you check this with another powered device such as an external HDD, router, printer, camera, or whatever?
I wouldn't entirely rule out a power issue just yet, even though your USB extension did not have a device attached, it still consumes power, albeit in small quantities.