Not sure this post will make your day any easier, but here goes...

You might want to try and build a TEST workstation fresh from the image and install in the correct order, and see if that workstation has the same issue. If not, you transfer your files and transfer only non-SQL Server and non-SSMS settings to that new workstation. That would prove that it's likely a registry issue, although it won't prove exactly what that issue is..

If you really want to spend some serious extra time, you could then choose to compare the registries from the two machines, and maybe you find it, maybe you don't.... It could also be a corruption problem in the registry and sometimes, there's no finding that kind of problem.

The one advantage of this way forward is that you either discover that it's a bug, or that a fresh build solves it. Painful, perhaps, but cleansing....

Let me know how you make out...