The problem here lies in if you don't give your harvester enough juice to have constant power then the trees will always out grow how fast the harvester can cut them down. The larger the tree farm the worse it is and often all the saplings have to grow before the harvester can eventually get to those bottom logs.
It's just how the harvester works on large tree farms, it cuts the leaves, then the logs, then removes the stump, but if another tree grows mean while in the area the harvester is cutting it will start again on the new tree, then again, then again and will not stop. The only ONLY way to get this working right is to either make your tree farm smaller or make sure that harvester has a lot of power.