As you mentioned, this could be a software or hardware issue. In order to test your computer hardware will be to try another USB front panel, if this fails, I am afraid your motherboard requires service.
I recommend, contacting support lines at Intel.
Live Chat support at wwww.intel.com/chat and choose desktop boards line
Unfortunately there is only one front panel USB3 on the board. The 2.0 one I am using is fine.
Is there a known issue with the drivers maybe?
I am not aware of any issues with front panel and USB 3.0 ports. Try updating computer BIOS or wait for new drivers to see if this will be corrected.