Considering we are all having the exact same problem (Win7 & Win8) and that by entering and exiting the BIOS, the ports seem to work as normal and resolve the issue until a reboot, I would hazard to guess the issue could be resolved by an updated BIOS.
If an Intel tech is reading this is there any plans to launch an updated BIOS for this MB? Would it address this issue?
Otherwise at least we can get the ports to work with the 'temporary' fix.