For this kind of behavior, I would recommend you to test the system out of the chassis with minimum configuration.
Please make sure you installed 0039, since this the version contains the update for the Management Engine 18.104.22.1688.
BIOS v0041 and 0044 also include fixes related to USB ports.
You can also try to uninstall the USB drivers, restart the system and then install them again. The latest ones we have available are from October 2013 Download Center
I updated ALL of the drivers, and the BIOS. Same problem. No USB ports, except the mouse.
Please help. How can I get the USB ports back?