I just built this desktop a week or so ago, and I've noticed some problems when running peripherals on my on-board USB ports. It seems that the problem occurs whenever 2 are running at the same time, such as my dual band wireless N USB and syncing my iPhone. Either one will work, while the other fails, or neither will work. And to make matters worse, instead of just failing, it turns the device on and off, on and off. This problem hasn't really happened with my USB keyboard and mouse however. I've updated the BIOS and also searched for any kind of on-board USB driver for this mobo without any success.
Here's what I'm running:
Windows 7 Ultimate (64-bit)
Intel Core i5 750 - socket 1156 LGA
ASRock P55 Extreme
BIOS - American Megatrends Inc. Version P1.80 (10/30/2009)
2x2 GB Corsair DDR3 PC3-10700H (667 MHz)
NVIDIA GeForce GTS 250
I had similar trouble to the OP, with a USB mouse seemingly dropping signal every 10 seconds or so, and a USB portable hard drive that just power cycled on and off when it was connected to the comp, and no indication in Windows 7 that it was plugged in.
I updated the bios as suggested, to no avail, and fiddled with the USB configuration settings in the BIOS as well (with no luck there either).
I switched the jumper as suggested by CL3M, and after booting up the portable hard drive started working right away. Windows 7 finally recognized it, and I was able to access the files on it without a problem.
The mouse is still behaving erratically, and it works fine with my other computers so I'm still investigating that, but getting the hard drive working was a huge win.