Title pretty much says it all. Builder will build pumps with liquid already in them if that's how they were at the time they were blueprinted

Do not open an issue if you're not planning to fix it, instead open a thread on http://mod-buildcraft.com/forums/index.php?board=2.0

Indeed, the correct procedure is as @50Wliu noted. It helps a lot. In this case though, I'm taking ownership. Will fix.