" the server will hang for a minute and eventually repaints"
That one is a bit easier to answer. A server is not a client machine. It's job is to serve and uses such as logging in and the screen painting are at a very low priority compared to your average desktop.
I'm sad to read that someone used a registry fixer or cleaner on a server. I bet you know what the moderators here think of that.
I've never updated IE on any server beyond what is required for the server needs. It's a server and we'll only update the security items but not things any user would use since "it's a server."
I'd get rid of VNC too and slowly move the server back to being just that. A server.