Sorry, posted too early. More details: I have just set up a RFTools Miner in the Mining Dimension with a pump card. I use it to remove all fluids down to bedrock so that I can set up my quarry (vertical digger from AA) without leaving behind large amount of flowing fluid.
I just set things up and started. The problem is probably the fluid router from immersive engineering that I put on top of the builder. I want to void water an keep lava (ender tank on top of fluid router)