I have been working on this but have been unable to determine why it is happening. The parent form is deactivated at the point where the DocumentWindow.Dispose method calls the base Dispose method code in Control. So something in Microsoft's code is causing this to happen in this scenario. If there is any sort of focusable control on the Form (like a Button) when the document window is closed, the parent Form is not deactivated.
Since I'm not sure what is causing this, I've added a check to reactivate the parent Form if this scenario occurs. It will be in the next maintenance release.