Hello guys,
I have heard earlier about this issue from someone else, unfortunately I am not able to reproduce this issue on my setup. My Kodi runs full screen, not windowed, and I have not once had this issue, as I mentioned I understand it is happening as this isn't the first time I heard it, but without it happeing right in front of me, and without an error report in the Kodi log (which this situation wouldn't produce one) its taking me a minute to fix.
I did find one small line I thought could have been causing it and fixed the line in the last release 1.3, are you using the newest version? Have you tried uninstalling Kodi and reinstalling it? Are you using Windows 10, the last time this issue was reported to us the user was running Windows 10.
Syriacn