I can second this issue & hopefully be a bit clearer than OP for my situation. Fallout4 running Storywealth collection +extras. I got notification to update from the 11.7 stable to the latest beta (1.12.0?) As soon as Vortex finished the update I went from having 185 ESP to most, if not all of my my files marked as ESPs & it couldn't deploy cause I was over the limit. Tried to Ctrl-A & mark all plugins as light & it would very briefly change to 188 ESP & the rest light, then revert back to everything ESP & warn me it couldn't deploy. Just vortex with it's integrated LOOT
Opted out of the Beta program & downgraded back to 11.7 stable & everything was kosher again.