I shows up when I click on a package or folder. It occurs after a prolonged period of use. If I find a pattern I'll let you know.

I believe this was fixed for the 5.0 GA release. If you still see it, check your Window > Preferences > General > Capabilities, and make sure you don't have the individual WTP functionality enabled, in which case it is supplying a refactor menu so is MyEclipse.