Make sure "wake by USB".... or something like that, is set to disable in BIOS. Some motherboards keep supplying +5V to the usb ports even when shut off. This is normal. Simple solution: just turn off the power at the PSU. (the switch where the power cord is at in the back).
Also If you are running Windows 7 the USB ports can be powered down using Selective Suspend.
Start > Control Panel > Power Options (if not visible change view to Large Icons at top right) > Change Plan Settings (for whatever plan you want) > Change Advanced Power Settings > Change settings that are currently unavailable > Set USB selective suspend setting to Disabled under USB settings and then click OK to save the changes.
You may have to reboot.
Also, found this on Tomshardware: " I know this is old but I just found the fix for my H97 and it may be the same for the Z97. I went to Advanced>Deep Sleep and enabled it. Hope this helps if anyone is still stuck."
Also this: "Check in BIOS, ACPI Configuration and turn off USB Mouse Power and USB keyboard or other related. See if it working."
Good luck!