Currently, the motherboard is attached to the case only where I have used standoffs. I did not use the two standoff points that are closest to the I/O shield, and the I/O ports do fit into the IO/shield without a problem. I hope this works when I power it on. I don't intend to power anything on until I'm ready to install the OS which will be next week. Any suggestions/advice before then will be appreciated.
Check your manual for which standoffs you are suppose to use. Not all the holes available on the motherboard backplate are used by different types of motherboards; M-ATX, ATX, etc. If you did use the correct number of standoffs and in the right places I don't have a clue what could be wrong, but do know that you shouldn't power the system while you have it seated badly.