I think there are two possible causes.
1. There is too little presence of ground in the area where the buttons are. With my case, it is all plastic besides the buttons. The grounding wire is good, but it connects to the outter portion of the connectors only, and there is no shielding on the wires (which may not matter). A solution would be to add a bunch of metal that is grounded to the front area where the buttons and connectors are and to try to get it as close to the connectors and buttons as possible to ensure as much of the energy is released to ground.
2. The USB headers on this motherboard are overly sensitive to out of spec voltages or frequencies. Since the rear USB connectors are not affected, this would imply two different USB controllers on the motherboard, or at least two different physical designs.
I may try building a USB buffer to put between the USB header and front plate to see if that helps. I may also try adding shielding to the USB cable with the shielding grounded. I don't need the shielding so much, as the continuous presence of ground. The next thing I may try is to put a ton of metal near the front of the case that is grounded to see if that helps.
There is a diminishing return, so I may just disconnect it all and buy a 5.25" media reader with USB ports and see if that solves the problem and just ignore the front USB ports. I haven't decided yet, I don't have the time to solve problems like I used to.
Cheers,
Scott