That's just how the buildcraft quarry works. It will fill every inventory slot connected to it - that includes engines and whatnot. I usually place my engines few blocks away from the quarry to prevent this.
Also late to the party but I'd like to share my solution to this as well - just IC2+BC.
On the right side there are chests for depleted cells and coal dust - we like to keep a huge supply of them.
Next is the buffer chest so we don't have to worry about overflows spilling.
Reactor chamber has an emerald pipe connected to it configured to pull out recharged cells and store them away.
When there's any vacant space inside the reactor the gates kick in and temporarily turn off the reactor to get maximum efficiency.
Reactor also gets turned off when the buffer chest is empty and is waiting for new isotope cells to be made.
It could probably be made fully automatic but as we have a double-chest full of recharged cell stacks there's not much need.
BC emerald pipes are a godsend.
Hi. I've found a bug when trying to automate our server's breeder reactor.
Here's the side view of relevant part of the reactor setup:
:Reactor: - reactor(chamber)
:Copper Ingot: - copper wire
:Lava Cell: - buildcraft pipe with a golden gate on it
:Reactor: :Reactor: :Lava Cell:
:Reactor: :Copper Ingot: :Copper Ingot: :Copper Ingot:
When the gate has been set up to detect reactor ideal breeding temperature and I right-click on it the server crashes. But when I remove the piece of wire directly underneath the pipe all is well. Crash report can be seen here: http://pastebin.com/YKJ1cQmM