Cinema display lost the 3 usb ports after running cleanly mac 3

After installing and running cleanmymac3 my thunderbolt cinema screen has lost the function of the 3 USB ports so my usb external hard drives don't appear in finder.

I know they are OK cos when i connect them to the usb port in my mac they mount successfully

Anyone know what to do and how to fix this problem

I guess I could reinstall El Capitan again?