I tried to add pd (millers vanilla) to homebrew/caskroom yielding some errors. Here is what the developers say:

"Hey there! This repros for me locally, looks like Pd-0.46-5-64bit.app comes out with permissions 555

dr-xr-xr-x     3 phinze  staff   102B Jan 19 17:43 Pd-0.46-5-64bit.app

So the cleanup operation after extraction is failing to remove the temporary dir.

Would it be possible to work with the maintainers of pd to get them to repackage their tarball with proper permissions? If not we can look into seeing if Cask can proactively chmod all extracted tarballs, but that seems like overkill if we can just get the maintainers to help us out."

--