I was having the same issue of SSMS crashing several times a day and opening as many as 50 query windows when it SSMS managed to launch. I found an article - here I think - that told you how to turn off the automatic opening of windows on launch. I even closed every window when I did get SSMS to launch, then closed SSMS in the hope that it would not try to open windows that were not open when SSMS closed, but that did not help.
I have only been running with the auto-load off for a few hours, so it may not hold up, but it was getting worse and worse, and I've been up for longer now that I had been before the change.
I'm running SQL Server 2012 SP1, CU4 on Windows 7 Pro, with the databases remote.