Did you loop your Energystorages? If so, then it's your fault as loops are not being processed by the E-net because of infinite senseless Energytransfer, which could even lead to terrible Cable-Loss, while just storing EU.
I did loop but the issue was a different one: the enet behaved unpredictable, sometimes drawing energy from the one box until machines went dry even though the other box was still full, then suddenly after reloading the energy was drawn from the second box but the first one was ignored.
Expected behaviour: Energy is drawn from both boxes by machines and excess energy is stored in the second then first batbox.
For clarification, this was about my setup (side-view):
Left batbox output pointing towards machines only, right batbox output looped bat into the enet.