Update: It's not the rushing alert, it's the "enemies visible" info window. If it would appear because an enemy just became visible, on the same turn that any other menu is about to open (e.g. terminals or level up), something gets conflicted and the game stops accepting input.

Easy enough to turn off every run, but annoying to have to remember to do.

I haven't been able to tell for sure, but I think this mod causes the game to freeze if the enemy alert would appear just as you're accessing a terminal. I've had that happen several times, and the only thing to do appears to be to force-quit the game and reload from the (hopefully-made) auto-save.