What case are you using?
If you have a case that doesn't have built-in standoffs and don't install them, there's no way the mobo would sit high enough for the rear IO panel to fit through the back faceplate. All standoffs are the same height for this reason. Otherwise cases and motherboards wouldn't be interchangeable. I have occasionally seen a random "tall" standoff or two stuffed in an accessories bag, but we're talking ~8 regular height ones (enough for the entire mobo) and a single tall one. The tall ones stand out like a sore thumb compared to the rest. Not sure what they're included for.
Oh, and don't over-tighten the mounting screws into the standoffs or you'll have a hell of a time getting them out. I had this problem in an old rig where I went to remove the mobo screws and the standoffs unscrewed from the case instead of the screws. Two fingers on the stem of the screw driver is plenty and/or use a drop of loctite on the threads of the standoffs.
Main: i5-3570K, ASRock Z77 Pro4-M, MSI RX480 8G, 500GB Crucial BX100, 2 TB Samsung EcoGreen F4, 16GB 1600MHz G.Skill @1.25V, EVGA 550-G2, Silverstone PS07B
HTPC: A8-5600K, MSI FM2-A75IA-E53, 4TB Seagate SSHD, 8GB 1866MHz G.Skill, Crosley D-25 Case Mod