I built it in 2010:
NZXT Apollo Black ATX case
GIGABYTE GA-790XTA-UD4 mobo
AMD Phenom II X4 965 Black Edition Deneb 3.4GHz CPU
CORSAIR Enthusiast Series TX950 PSU
Intel X25-M Mainstream SSD
Western Digital Caviar Black WD1002FAEX 1TB storage drive
4 x 2 GB G.SKILL DDR3 1600
LITE-ON 24X DVD Writer Black SATA Model iHAS-324-98B
MSI R5870 Eyefinity 6 Radeon HD 5870 2GB video card
Since I have run into this problem I have replaced the PSU, and mobo, without luck. I have also replaced the case, but I cannot recall if I even had the card reader that holds this particular USB port while this problem existed.
I would still do as suggested above; disconnect the problem ports from the mobo hearders and see if the problem persists when you touch the ports. That will determine if it is a wiring issue from ports to board or if it is an ESD issue only. Do you have a VOM meter like a Fluke?
Since this is the 2nd case, it unlikely the problem is in the case's ports wiring. The mobo would be the only other culprit.
But... The more I think about the situation, the more I;m thinking it's an ESD issue. Before you do anything else, try grounding yourself by touching some bare metal on the case before and while touching the ports. See if the shut down issue is avoided.
OK, that seemed to do the trick. By opening the case and touching metal with one hand, then plugging into the jacks and USB port I was able to use them w/o the computer rebooting. Even after taking my hand away from the metal, then plugging into the jacks I was able to use them with no problem.
My next question is ... what do I do next? It is a little impractical to open the case like that every time. A little info that may be of use: my case does sit in my office on a carpeted floor. I sit at my desk with my chair on one of those plastic chair mats. Also, my computer is plugged into a Cyberpower 1500AVRLCD UPS. Also, the whole house has a surge protector on the fuse box. Thanks!
Surge protection and grounding are somewhat separate issues. The former protects equipment against electrical spikes in voltage, the latter allows dangerous stray currents to discharge safely to earth. It appears now that your problem is indeed ESD.
Apparently your plastic mat is allowing your body to build up a static charge until you find something grounded to touch... so if you've accumulated enough of a charge and touch something grounded, it will discharge to earth. The delicate motherboard circuitry senses the ESD because the USB and audio wiring is close by the grounded port.