The cables used by the front panel's USB ports may affect the USB ports speed.
If the cables are where you can see the wire colors all the way from the motherboard to the front panel's USB ports, it will most likely revert to USB 1.1 speeds when connected to the motherboard's USB 2.0 headers.
If the cables are where you can only see the wire colors at each end, and the longest middle portion of the cables are in a single colored jacket, then the front panel's USB ports should operate at USB 2.0 speeds when connected to the motherboard's USB 2.0 headers.
I have had several cases that had the all wire colors visible cables, and every one of their front USB ports would only work at USB 1.1 speeds when connected to USB 2.0 headers.