In response to Kingfish as it seems to have been deleted.
I could disable these two programs yes, I don't use raptr unless I'm recording and now keep it closed due to the problem. Windows wont read battery levels from the Logitech mouse, thus it will likely die when I'm gaming or something. If I open Aquasuite or something else that's low level then I will still have the same problem. The answer isn't to just not run anything.
Another more pressing issue is having Crossfire enabled when I want it disabled via CCC in certain applications that Crossfire conflicts with.