Are you sure they're turning into the harvest stage and not the mycelium stage which is one of the biggest problems?
I've had six gardeners since the patch. One of them would plant things which then went through an extra growth stage (mycelium) that is supposed to be mushrooms only and as soon as it was done it would go back to being a sprout then continue it's cycle. Having supernatural installed seems to have corrected this issue because now I actually have mushrooms in my game and I haven't seen it happen again.