When wooden pipes are placed next to quarries, they can pump quarry frames. This is not an expected setup, and easy to workaround, but should be fixed. See various reports, in particular http://mod-buildcraft.com/forums/index.php?topic=805.0

I'm very confused Toad, I'm the same guy that reported the glitch. Did it get solved?

@Amaster151 nope - it's reproduced and understood. At this stage, it is scheduled to be solved with 6.1.1 (6.1.0 being the one before, not yet released).