Building C (Cython?) code causes build to happen twice, but not three times

Before activating the helpers, astropy only had to build once, and afterwards, *nothing* got re-compiled unless it was changed.  With the helpers, though (after #11), now building once compiles everything, but then *some* modules re-compile when you build a second time.  Third and subsequent builds require no compilation.

I've included build logs for each time at https://gist.github.com/eteq/e2e3f0a4b443d2123949 both for before and after astropy_helpers was added to astropy. Note that each one is in a separate file, but th first one is very long, so it requires a lot of scrolling.