I was also having issues getting nothing back when throwing saplings into a mana pool.. Turns out my Endoflames were eating the saplings.
True, my Endoflames are like 3 blocks away from the pool. However, they do have a small delay when gobbling up the coal pieces/blocks I throw at them; do they use up the saplings instantaneously?
Getting cactus (and other flowers) requires that you level up the crop first. When I sheer a 10.10.10 cactus I get 4 cactus so I figure it has to do with it's drop rate but you can't get one cactus so you have to wait until the drop rate is 2 or more.
Thanks for that info, didn't think of leveling up the seeds to get the blocks.