I am also playing next to them every day, my base isn't that big. The timers are either frozen or completely off!
Edit: Just a thought, but could trees be getting 'stale', meaning that their production rates get slower as they age? It wouldn't make sense, but it could be a sadistic way to force us to cut the old ones down and become more productive with our man-made forests! It could also force us to commit crimes against nature (who knows if cutting down a tree is a crime? what about a sapling?).