Hi there! I got to this post googling for a solution for my system. I have almost the same issue, just that it does NOT affect my computer on startup.
I get exactly this Desktop-Folder-Window just randomly then and when. It pops up in the middle of the work. It puts itself over the active window. It does not seem to be related to any open software or any particular user action, its really just random...
Sometimes it does not happen for a while, and then, however, it starts again. We talk about 1 new Window popping up in 5 minutes or so, sometimes more, sometimes less.
As it does not happen when starting, in my case at least, its probably not a startup-entry, as it was suggested in the previous posts.
Aero Peek is off, as I prefer to use the old fashioned windows classic theme.
Thanks for any useful help!