I only just started using these 2 programs myself, but I have also come across the same problems. However, I noticed a few things that may be of interest.

When first loading up map viewer, this problem will occur. You will be able to record videos using WeGame, but will not be able to move or toggle anything on/off using the keyboard. However, if you then do anything that causes the map viewer window to lose focus (ie. alt tab to something else) the keys all start working again. However, you will now be unable to record videos, even though the green WeGame square in the top left doesn't disappear....

Another strange thing I noticed is that windows explorer seems to crash and then reload if I open the WeGame videos folder while it contains one of the videos I made in map viewer. If I delete the files, I can open the folder fine, and it appears to ONLY be videos from map viewer that cause this problem.