This may be the way I'm using them since couriers are not working I have a buildcraft pipe pumping out of the top inventory. Saplings when picked up by machine go there first and the buildcraft pipe pumps them out. If I shift right click from my inventory how ever they go straight into correct boxes

Hmm...they should auto-place the saplings into the 'resources' slots (the 3 middle ones).

Will investigate this shortly, should have an fix available for next release

This function appears to be working properly -- saplings picked up from the work bounds are going into the middle slots as they should be. (Might have been another recent fix that also fixed this..)

Will be closing this issue shortly unless I can confirm / get more information to help me duplicate it.

It appears to be fixed now though I had to break replace the tree farm

Thanks for updating the issue. Will close for now -- please re-open if the problem persists / can be duplicated / more information is found.