Have you tried the RP2 Filters? Set them up next to the separator with an empty cell as a filter and it should pull them out for every redstonepulse it receives.
Yep. Also tried the retriever and the sorter (also with an empty cell inside). They didn't seem to work either.
Does anyone know if it's possible to extract the empty cells out of the Isotropic Separator with either BC pipes or RP2 tubes? I've only managed to get the filled Deuterium cells out (or nothing at all) after trying all six sides with both BC and RP2 pipes/tubes. I've been trying to build an automated re-fueling system for the fusion reactor, but it's kinda difficult when the Separator gets clogged after only producing 6 fuel cells. So is this a bug, or did I screw something up? 
In case it's needed, my currently installed mods are:
Modloader
ModloaderMP
MCForge 1.2.3
IC2 1.43
BC 3.0.4
RP2 pr4b
Rocket Science 0.71
Railcraft 2.2.1
TMI
