I mentioned this same issue which occurs when the NL PLayer is in windowed mode; I should've mentioned this long ago but this also occurs with all versions of the Flexitoolkit. You cannot alt-tab into the program; it simply does not appear on the menu.
Does anyone else have this issue? It doesn't happen for me (on Windows 10).
The latest updates to both the player and Flexi should fix this. I would assume GSTool probably has the same issue, I will make the change in the next update.