I've had similar problems as well when working with conjunction with miners. So, I decided to test it out with a new flat world. Here are the screenshots that I took. Hopefully this well help with solving the problem, and if anyone needs clarification, I'll do that to the best of my abilities. Because I really am sick of having to break then re-install every time.
This is where I had set everything up and started working. It dug 2 water blocks down before it hit bedrock, so the miner stopped. This one here is of the pump. See how there is one cell missing from the stack of 64? this is where it went. But what I wanted to know was why it wasn't digging through water like it was with lava. So, I had set up another one where it was ONLY water, 3 blocks down from below the pump, and a constant water source. You can see that here. However, it wasn't working, just like with the one by the miner. It would fill up, and stop working. I then noticed that the lava had only one layer before it continued on with other items. So, I decided to replicate that with my water like so. When I did that, lo and behold! The pump works perfectly, spewing out water cells. when I took out that lone dirt block like so, it stopped working again. I tried the same thing with lava, but because the way lava works, it didn't work as well as I had hoped...
So.... is there any way to get around this? or is this just something that'll never get fixed?
And I'm sorry if I necro'd this thread, but I've looked EVERYWHERE on the net, and this is the closest thing to my current problem... everywhere else it said that they were also using buildcraft pumps/pipes, and my comp couldn't handle both buildcraft and IC2.