I have a pipe feeding from a ender chest with one cell, its not taking the item out of the chest but adding it to the overall capacity of the ender cell.

I can confirm this behavior, that when there is a non ender cell in the chest, rather than just adding to the cell as it does when using the UI, I hear the ping of it being added to the ender cell, but it isn't removed from the chest. This also happens when a battery is in the chest. It doesn't seem to matter what kind of chest is used. A logistical transporter does not exhibit this issue, nor the IF item transporter, but it does also happen with the Ender IO conduit