Mine Is doing almost exactly the same and I've got the same info. Only difference is I try to do them manually and 2 things happen that I don't understand. Firstly, it takes about 20 times before it works (which I always understood to be random anyway but this is never random, just takes a long time every time). Secondly, whether in the deployer or doing it manually, my bonemeal count doesn't go down on each click (or animation of when just holding down), it only uses one once the tree grows.
I didn't want to post this as a bug until I found someone else with the same issue.