I used to power down my PC every night. However the folding@home project has lead me to keeping my PC on. My CPU and GPU has been running at 100% 24/7 since last Nov. My CPU has been working around the clock for even longer.
I don't use Recycle Bin for storage. If I delete something, chances are very high that I don't want it on my PC. The sole purpose of Recycle Bin is to give users a way to recover from deletion. Anytime you find the need to recover from deletion, it is always easiest if there are few files to search through. It is my opinion that keeping things in Recycle Bin is poor maintenance skills. If you need the files, place them elsewhere and use Recycle Bin for what it was designed for.
CCleaner is an excellent way to keep your PC clean of files that are not needed. Not only does CCleaner empty Recycle Bin, there are many other areas of the PC that is cleaned as well. It just so happens the newest version seems to have a slight side effect with Microsoft Security Essentials.
Now that I know whats going on, it doesn't bother me as much. At least now I know it is something that I did to trigger MSE's status change. Since MSE is not the issue I'm marking the thread solved.