I'm having a very strange problem.

In advance, I apologize if this is not the proper place to post this.

All of these problems happen all at once, after a few hours of use:

1.) My Recycle Bin will disappear upon emptying it.
2.) All of my folders contain invisible icons. Not all of them are invisible, but most of them. Those that aren't just contain the standard file icon (white piece of paper).
3.) My Desktop will no longer show thumbnails for images placed there.
4.) "My Computer" won't load. A green bar just moves across the top and no icons appear.
5.) The "Libraries" directory on the left of explorer won't load. They show the magnifying glass icon.
6.) Appwiz.cpl (Add/Remove Programs) loads very slowly, or not at all. Green loading bar again.
7.) Desktop gadgets disappear.
8.) Rebooting explorer causes this error message to appear upon trying to open folders: "The remote procedure call failed and did not execute."

Restarting Windows seems to repair the problem, but it comes back later. This ever happen to anyone else? I'd really like to rectify this without having to reinstall. I mean I will if I have to, but I'd like to think that's a last-ditch solution.

A good virus scan with SuperAnti Spyware and Malwarebytes would help too.

I have no restore points to go back to...trust me that was my first idea. :/

I've tried SAS, MalwareBytes and ComboFix. No help.

I'll try System File Checker.

Windows Resource Protection did not find any integrity violations.

The problems are so unrelated that it is difficult to find a pattern. If it is not malware (since your scans came out clean), it might be a conflict between processes.
For starters I would disable all startups (except AV). Then watch closely when this starts to happen and what programs/processes you might have started preceeding the problem.
I don't think there is a silver bullet to solve the problem. Just elimination of possible causes.