I've found that while watching fullscreen movies (media player classic - other players are untested) Citywatch popups do not vanish until I move the mouse. I've also experienced issues with Civilization Beyond Earth where a Citywatch popup will cause my PC to produce a black screen that forces me to reset my PC (alt-f4, ctrl-alt-del, alt-tab, win-tab, ctrl-shift-esc key combos make no difference). The second one might just be my PC configuration as I'm using a rather old 32" TV that's really particular about its resolutions though.
What I propose is one of two things:
1. An option within Citywatch so that when an application such as a movie player or game is in fullscreen, notifications are supressed until fullscreen is exited.
2. A "supress notifications" button for city watch that will turn off all notifications until it's unticked.
Option 2 is much easier to implement as it does not require city watch to know the current status of the computer however it is less user friendly. I do realise that I can sign out of city watch to gain this effect, but in doing so you also lose the mouseover functions. Personally I think both features would be a useful enhancement for the application.