I understand that your Intel(R) Desktop Board DH67CL will have 2 bad USB ports and you will like to know how to troubleshoot them.
Each USB controller will handle 2 ports, it is consistent that if the controller fails you will loose 2 ports.
In regards to your inquire, there isn't much troubleshooting that can be performed.
I recommend you to update your BIOS via F7 method and test the motherboard out of the chassis.
If the problem continues check for burn marks and contact the warranty department
Well, an update of sorts. Shipped the board in for service...a week later got the board back with the exact same problem. No email, no phone call, no letter discussing the issue or the testing that was done to the board, nothing. Chatted with customer service Friday to find out what the deal was. Turns out the 'warranty center found no issues' and it was recommended that I do more testing. Fine, tore the system back down for a bench test. This time to bare minimum...stock cpu cooler, on board video, no frills. Same problem, top two usb ports don't work. I've reset the bios and tested multiple devices and what I have determined is that the ports in question will power up some devices but absolutely no data transfer or OS activity. Usb laptop light will light up, external hard drive and DVD drive will power up and my phone will charge via usb data cable on these ports. They won't charge my mp3 player and won't power up an external floppy or a usb thumb drive. So yeah, as soon as I can get access to customer service again, I'm gonna attempt yet another service claim. I think this time I'm gonna include explicit description of the issue cause they obviously overlooked it the first time.