There are metal tabs on the I/O shield. That are supposed to rest on top of the ports blocks to ground them. You are supposed to angle the board when you install it so the board slides under them and they are in contact. If you don't you will bend the tabs flat across the ports and not be able to plug anything in.
You need to unscrew and move the board back an inch or two, bend the tabs back where they belong, and install the motherboard correctly.