olchaos There are a few threads in the Feedback forum about the pop-ups, if you want to add your "vote" there. I doubt EA is going to do away with ads anytime soon, but it doesn't hurt to ask.
As for your particular issue, I don't know what to suggest since the problem is self-correcting, eventually. I guess you could play in windowed mode for a few sessions after each patch or when something else new appears on the screen. Offline mode in the EA App is also useful.
I've never had this issue myself so can only go by what other players report. Sometimes it's definitely the mods, sometimes it's a bug, sometimes it doesn't have an explanation and using windowed mode fixes it reliably enough for the player to not want to investigate further.
maybe is a directx 11 issue. never tried dx9. maybe when a patch is coming will switch to dx9 and if the problem gets solved maybe is a layer issue that is not properly implemented/compatible with dx11 but does work well with dx9
