I recently installed the 1.23 version of IC2 and put in a mass fab. I use buidlcraft for the pipes and found that you can only extract UU-matter from mass fabricators by piping from the bottom of the machine.
The sides and the top just remove any scrap that is currently in the machine.
I don't mind the current setup as I can still do what I need, but it is just different from every other machine letting you extract items produced from the sides.
Great mod, it has outlasted EE for me. I uninstalled it :).