Update: Final release V 1.0 seems to have taken care of the problem. The following change, "There is now a disable mode switch message option in the "Map Controls" dialog", appeared to fix the problem nicely. By clicking the box to turn off the Messages, the annoying pop-ups stopped. I suppose that this might be helpful information for a new player, but after a certain point, he'll get tired of always being reminded that he can move the clipboard with his mouse.
Thank You Skuzzy for fixing this! It was so annoying having to deal with having a pop-up blocking my view of something 10 - 20 times in every mission.