I don't have Buildcraft installed, but it works with Electric Sorting Machines, Item Buffers, and Chests. (I use the Electric Sorting Machine) Maybe you set the Ejector Upgrade to the wrong side? You only need one, by the way. Also, make sure it is the yellow Ejector Upgrade. In the worst case, Buildcraft pipes may not work (if that is so, it probably deserves a bug report). Finally, this thread may have a better home in the Support forum.