I presume you’re describing an old issue that got worse in version 5, and has never been corrected ever since.
I don’t believe it’s directly related to ‘objects having been selected’. I do believe it mostly has to do with various command function activations, completions, dialogues etc.
My usual ‘hurdle over the problem’ is to quickly click with the regular mouse into an empty spot in the workspace, in order to correct the glitch.
Sometimes you might even have to invoke a regular rotation with the regular mouse to correct the glitch.
This used to be very frustrating to perform every time to mitigate the issue, but things like this can become subconscious after you do it a million times 
It would be great if the world we live in would finally accept the 3D mouses, but they’re still waiting for something …