Exactly as it says. For some boneheaded reason, setuptools (and now distribute) easy_install sets the +x mode on every single .py file in the bundle, not just the ones marked as scripts.
What this essentially means is that any package that would like to rely on nosetests' auto discovery features is up a creek without a paddle, since nosetests ignores executable files by default, e.g. see e.g.
I should mention that this behaviour does not appear in pip, and I believe pip got it right.
This is a long-standing bug in setuptools, and I can't think of a conceivable reason for anyone to be relying on this broken behaviour; it might even be a security issue for the installed package. I thus propose it is a bug and should be fixed.