One of my teammates had some problems with NetBeans and cvs, as even if she checked out all the sources for a project from scratch NetBeans still informed her that some files were unknown to cvs. That was strange, as cvs just provided them all. Everything worked fine on every other computer, and the repository seemed all right.
After some head banging we resolved to check the NetBeans configuration directory, and... tadaaaaa... we found the $NetBeansVersion/var/cache/cvscache directory, full with nice and likeable binary files. Being aligned with all the rest, we simply emptied the directory and everything worked fine.
More a reminder than a real post ;-)