I ask EVERYONE with a motherboard with a Wake From Sleep issue... 
Are you plugged into Intel SATA 0? 
I was brainstorming as a programmer and thought ... "hmm, i'd probably hard code that to SATA  0 as a presumption. "
I moved my cable to SATA 0 and ironically, that worked. 
Are all of your boot drives on SATA 0? 
Please everyone check and post your experiences. 
I'm on a GA-x79-UD5 . I once didn't have this issue, then I reworked my board, updated drives, moved to an SSD, and later in those issues, i never really paid attention to my cables, i had nothing plugged into SATA 0/1 for a while, no particular reason, sometimes had the BD.  plugged into it, no reason. 
But now, with my boot drive plugged into INTEL SATA 0 (there is also a Marvel controller for ACHI/IDE/RAID) i've repeatedly worked, gone into sleep for a couple minutes, half hour, 2 hours, etc... and it's waking from sleep from mouse or keyboard and they are both USB, same ones it would infinite boot loop in before. 
Again, please let everyone know your results.