It looks to me like this is more than likely a bug. I would definitely go through your VAR on this one. They should be able to diagnose and\or repair it based on your system.
Please see this thread and the two other threads that John Sweeney refers to. This is a rare problem which we are unsure of how it happens, but we believe we have it fixed in SolidWorks 2013 so if it detects the problem, it fixes it itself. These threads should give you specific information on how to edit your registry to fix it.
I hope this helps,
Thanks a lot! I played around with the registries a little bit as John Sweeney suggested and got it working. Specifically, I set the Dock State binary value to 31 (which sets the "Data" value to 1) which oriented the Command Toolbar along the top. If what Mr. Sweeney speculates is true, doing so likely resynced the faulty registry values and fixed the problem.