I have a Microsoft mouse with the same phenomena and it turns out that the middle mouse button on my Ms mouse in fact isn’t a normal middle mouse button. By default in at least Windows 8 it’s used to open a view of currently running windows, much like Alt+Tab in windows environment, however in TF this function is blocked. When I connected a normal mouse without any special functions it worked fine in TF.
So check what happens with a middle mouse button click in Windows to see that there isn’t any special things programmed on it.