Well, ive been having trouble with this too...
I made a 3x3 dirt panel, with an harvester and a planter. This Worked pretty well to start with, but as the system went going it didnt get enough rubber tree saplings back for some reason. There were no overflow, i used an AE storagesystem with export busses and imports..
As far as i am now ingame i use UU-matter to produce it, but it would have been more nicely to have an automated process for it!