Creating a custom library part in EagleCAD and avoiding DRC Errors
Yup, that's a issue with Eagle, at least as of version 5.  It would be nice if you could tell the DRC check to ignore anything resulting from stuff wholly inside a package, but you can't.  There has been talk of changing that, but I don't know where that is at with regard to version 6.  It doesn't matter anyway since version 6 isn't ready for any real use yet for a while.