One thing to check is in Device Manager, if you right click on some of the USB Hubs, there may be an Advanced tab. If there is, go there and use the Reset option. Perhaps it will restore the function.
If that doesn't help, perhaps uninstalling the current drivers and checking the box to remove all driver files might allow the system to reinstall to a workable condition. Since you have already tried this and there are not problems indicated on those devices, it may not really help.
You might also check msinfo32.exe and check the problem components section to see if the USB ports are listed.
The Event Viewer may have some information related to these also if you are getting errors with plugging in some device.