DuBlue,
Well, I just installed Calibre 2.2.0, and ALL of my plugin icons disappeared. I was on Calibre 2.1.0. Apparently this is a Calibre 2.2.0 phenomenon. I have had zero problems like this since I released my first plugin on Calibre 1.40, all the way through to Calibre 2.1.0 on Windows 64.
I am reverting to Calibre 2.1.0 from
http://download.calibre-ebook.com/2.1.0/ to see if it clears this up.