I managed to solve my problem meaning I was able to check the problematic harddisk (no errors found) and the Action center's message doesn't show up anymore. But I can still reproduce it. Weird thing is that this harddrive only contains non-active VHD, hyper-v's xml files and ISO files.
My pc has a main SSD and 2 normal HD's. I tried to do a manual checkdisk (from the drive's properties window) with each of them and 1 of the normal HD's also caused checkdisk to go into the CPU hogging mode (no sign of the fsavailux process but taskmanager showed a COM process hogging it).
I'm 100% sure there was NO drive activity during the 100% CPU hogging process. Taskmanager and resource manager didn't show any activity and I couldn't hear the drive rambling and certainly not for more than 15 hours (total cpu time reported by taskmanager).
EDIT: http://imgur.com/PBqyHj5 screenshot made with Process Explorer. I created a memory dump too, if anyone is interested let me know how you want to receive it (30 MB zipped).