Wow, steep learning curve for the tubes. I desperately need a way to turn this frustration into fun, cause it seems like its too much more of the former and not enough of the latter with tubes AND pipes. I'm just thankful I started playing after Logistical Pipes weren't available anymore. Had I been exposed to those, I believe I may have thrown my system out the window by now...
Anyho, there may have been changes since you posted. I had the regulator on top of the arboretum and I kept getting sand in the regulator. Placing a tube in between the regulator and the arboretum seems to have solved that. Also had to place a restriction tube between the chest and the relay [only two tubes until it gets further automated], otherwise no saplings were getting to the regulator.
Something else I noticed. I used what I learned here and converted my farm/combine tower to use RP tubes, since the BC iron pipes with gates weren't detecting full seed inventories. The only difference between the tree farm shown in this thread and my tower, besides that it's multi-level, is the regulator is going into the side of the farm, instead of the top as with the arboretum. Everything works fine but after awhile, like when the farm gets full of seeds, the regulator starts collecting odd amounts, filling up it's input side and then it's buffer...not passing anything. I say odd, cause I've tried to fix it and I've watched it take only some of what's being passed to it. There's also plenty of room in the chest. Wiki says I can pass seeds from any side to the farmer. Do they actually need to go into the top?
Wow. Yeah, seeds? Any side is fine [pffffft]. Who knew the farm had a waste disposal compartment? Also, how is this machine randomly generating sand? Think I solved it but I had to tear down my tower to do so. Also lost 1/2 the growing areas. Solution seems to be to feed the seeds in to the top of the farm but, with a tube in between the farm and the regulator. When the farm's full of seeds and the regulator gets sent some seeds, the regulator will refuse the seeds and turn redstone on. Any more seeds sent out by the relay will continue to visit the regulator. Once space for seeds in the farm becomes available, the regulator will turn redstone off and allow seeds to pass again. Hopefully no more problems with farms storing seeds as "waste material". With this method, farms need to be spaced 3-blocks apart [as in 3-blocks in between each farm].