SOURAPPLE Thanks for your comments! All of them! The issue you talk about is listed in http://code.google.com/p/sourapple/issues/list and is a known bug. I have yet to find out how to handle the cases where the App had been installed under Applications.
You say you couldn't remove any package, I will double check it but... were you removing a "problematic" package (see paragraph above) or just a normal one? It would be great if you filed the bugs in the page referenced above.