So try logging all devices out of iCloud, then logging back in. Can't hurt, may help.
Didn't work. I signed out of iCloud, Messages, and FaceTime on all my computers (two macs and a windows), an iPad, and an iPhone. They were all on for maybe 15 minutes or so then I figured what the heck and shut everything down for about an hour and a half. First thing I signed back in on was my mac mini and it showed the storage was still there.
I first noticed things were odd when I was running the IOS 9 beta on my ipad. I had to rebackup my ipad from scratch (figured it was some new icloud thing) and it would show in iTunes the last iCloud backup for the iPad was in 1969, which I interpreted as "I have no clue when this backup happened but I see something". Then when the GM version of 9 came out I removed the ipad from beta program and installed the GM version of IOS 9. Then iTunes was showing the right backup date. So my theory is my icloud backup back when I was on the IOS 9 beta is still there.
Since people have mentioned how waiting 3-5 days for the disk usage to update I'm going to give it a week of no icloud backups. Then I'll try removing my ipad from everywhere and completely unlinking it from my appleid and leave it like that for a few days.
As a quick update I found this lengthy thread about it. Looks like I need to call support and have them release the reserved storage on their side. Just need to find some time to actually call them... https://forums.developer.apple.com/thread/5246?start=105&tstart=0#discussion-64071