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1)at gnome login, after entering password, the error message: you are running the GNOME file manager as root. As root you can damage your system.... (and so on) even though file manager does not launch at login (it used to but was disabled with 'save settings' at shutdown) also there is a pretty long delay in launching file manager.. about 20 seconds to get the error message, then file manager launches normally. history: file manager launched at boot each time, until disbled using 'save settings' at shutdown. the long delay began, i think, after config of squid-2.2STABLE5 proxy server.
I think I know the answer to this one, so I will comment in hopes of getting you an answer before the RedHat staff returns from the weekend: In section 13.1 of the RH Linux 6.1 getting started guide, we are told that the gnome file manager is the entity that provides the gnome desktop functionality. The file manager window is just a subsystem of it. Even if you set your desktop settings to not display the file manager window when you log in (as I also have done, I use dired under emacs for most of my file management) the file manger is still running to manage your desktop. And, you can still make mistakes that can clobber your system, since you can have links to anything on your desktop. So you still get the warning message.
Indeed, that is correct. the file manager controls the desktop, as well as the windows. If you want to disable it, you need to go to Startup Programs in the control-center, find gmc, and remove it. However, you should heed the warning given by the message. You really shouldn't be logging into X as root. Log in as a user and 'su' to root if you need to do something.