I have suffered many times from such weird behaviors.
It turned out there there eclipse p2 updated mechanism is a total mess when you not using their way.
My advice is painful but this is what only way it worked with me.
Install a fresh copy of ganymede, add the .link for the nightly build then add any other plugins .....
If you you want to to update to another nightly build ,,, repeat the process.
Wouldn't be cool if JBoss had an update site for their nightly builds ?
wouldn't it be cool if eclipse update managers weren't breaking sane stuff ;)
We are working on getting a updatesite for nightly ...