Note: though you think the node is not in NCM it may still there really...
I've found that if I delete a node in NPM it stays in NCM, but unfindable through the webUI.
I have to go into the database and manually delete the entry from the database manager.
here is the query I use:
SELECT n1.agentip,n1.nodeCaption from NCM.dbo.nodes n1 where corenodeid not in (select nodeid from NPM.dbo.nodes n2)
[replace NCM and NPM with your database names]