Open the server's admin console. Delete the projects from the web based admin console for the server, not through RSA. The RSA GUI isn't removing them from the configuration.
You should be able to get into the admin console by right clicking on the server from RSA and selected "Admin Console" or something. Make sure you save any changes by explictly selecting Save.
I tried several times removing projects from admin console and add/remove projects and their combination when server is running/stoping/running kind of stuff, nothing worked.