I found myself a little stumped on this one - how do I remove a node tree from the startup.blend?
If you use 2.66: start blender (this loads the startup file in blender), delete the node tree and save the startup file either from the file menu or via ctrl u.
Check if it has fake_User. You see in the NodeGroup right of the Name a F - if it’s active, disable it, delete the Node and save startup (ctrl-u). otherwise see minoribus