I would triple check your connections at the motherboard. It sounds like you have something connected wrong, or the wiring from the front panel was marked wrong. Follow the wires out to see if they go where they are suppose to go on the front panel. And be sure your polarity is correct.
As for the USB and eSATA, as long as they are plugged into the USB header and SATA header respectively, there should be no reason they don't work.
If you are sure all of the above is correct, it would appear the motherboard is faulty.