I don't want to lead you on a wild goose chase, so if this is not related to USB 3.0 controllers this can all be dismissed, but sometimes XHCI controller/driver behaviour is the cause of various strange issues to users, and many have simply disabled the XHCI controller in the BIOS where viable, but I recalled this
openSUSE post where a user found a way to configure individual ports with the caveat - WARNING: all the below is chipset specific for the Intel 9 series. Just wanted to share that in case someone else finds it useful one day.