Thanks for the replies, sorry for my late reply. No chests was full, all ores are sent to different macerators and furnaces (1 for each ore), gems (redstone, nikolite etc.) are sent to a crystal chest, which is was about half full, all the rest was sent into an energy condenser to slowly produce diamonds. I did however find stacks upon stacks of dirt, cobblestone and sand randomly lying beneath the pipe here and there when I was lagging my way back to the quarries to shut them down. Overflow in the pipe, if that is possible?
What I ended up doing was removing them, and setting up a 32x32 grid on both quarries, which works just fine, I get no lag with this setup, neither any stacks of random shizzle under the pipe.