Zap is right, those jumpers on your mobo are for allowing the USB ports to be powered by the 5V SB. This is StandBy power. That means that if you choose to use this option you can have the USB ports remain powered even if the PC is off.
As for your front panel ports this problem is not that uncommon, especially with older cases. In every case I've seen it always came down to the quality of the front panel cables. If the cables are of poor quality and their impedance is higher than it should you get this kind of problems. I bet that that was the problem that made Antec get in the trouble of replacing cables, which BTW speaks highly of them.
I would suggest that you send them a mail and explore on the possibilities of getting replacement cables even if it's not for free. It would be a shame to stick with a pair of underperforming ports if you can avoid it.