I was halfway through making a selection (still holding in Left mouse button) when the updater window popped up, I clicked "Close" and let go of the left mouse button to finish my selection, but nothing happened. It seems when you are halfway through making a selection and a new window opens the selection wont end but just continue following your cursor. You can test this by holding the LMB and dragging a selection, without letting go, and with your keyboard opening "About" under the "Help" menu. Click "OK" and try and finish the selection. You can click both mouse buttons together and it will complete, but still.. you get the idea.
-Chris