I do have a fairly mod heavy game, but nothing that conflicts with each other. The problem is that some of my mods that require hotkeys (Smoking Complete, Zen, Camp Anywhere, etc.) or that have menus that need to be navigated (AMJM Wagons) stop working. Its not that the mods themselves stop working, it's that the hotkeys stop working. Even pressing F9 won't turn off PDO. The one mod that this doesn't seem to affect is Rampage trainer, but again, when the game is first opened, the other mods do work alongside it. It's just that they all eventually stop.
Please help, por favor.
Edit: Sleeping ingame ALSO seems to cause the issue, but is not the sole cause.
Edit 2: Actually, it seems to be my game minimizing for a second before continuing. As soon as this happens, all pop ups stop working.
SOLUTION: Turns out it had something to do with scripthook, I was using the one from the Nexus because it was supposedly the one that was working for the .18 update, but using AB's Scripthook has by far been the better option for me. Hope this helps anyone that was as confused as I was.