Because there are wires in there, they could be broken. You could have damaged a pin in the USB port, it could be shorted. When you plug in a USB cable, that metal could be bridging them. It might just be improperly built.
Are you saying it just doesn't boot with something plugged in, and that it works fine if they are connected after Windows is booted? Because that is a different problem. Might want to look at updating the BIOS on the motherboard and making sure the USB controller and that media card slot, etc are all up to date.
Any SATA cables plugged in to make that work?