Hi zeusxp, welcome to BC.
Those are two definete possibilities, though given a choice between the two, I'm leaning towards the motherboard myself.
Asus in particular had a real problem with the southbridge getting fried on some of it mainboards resulting in dead usb ports. I wouldn't start right off with any HW though if everything else powers up.
A missing or damaged .dll file, among others, will also cause the same issue.
Since you really should reformat after a new motherboard installation, I'd do that first just to rule out OS corruption. For me it's simple as I keep complete system backups on individual drives. I don't know what your backup situation is though. Using the Windows system restore function in this case wouldn't be a reliable indicator. You might also consider a seperate usb card installation though if it's the motherboard, I'd be wondering what else is going to happen.