Our client is running Centos 6.4 Desktop on a VM (can't upgrade). We were doing some updates to our software on the client machine. There are subdirs not showing in Nautilus. I can see them with an ls from the command line, but not in Nautilus. I know they are there, I can do anything I want with them from the CL, but the boss likes to use the gui and want's to know why these files aren't showing. I've restarted Nautilus, restarted Gnome. Can't get authorization to reboot the machine. There are hundreds of this exact VM and image in the client network, never seen this before.

Any ideas?

First Guess: It's got to be a permissions or $PATH issue. GUIs often use a system account, you probably use sudo root when you ls?

what are these UNKNOWN!!! files/folders?

I can not read your mind
( my crystal ball fell on the floor and broke )

the locations of the unknown folders would help

and posting the exact ls command will help

John VV: The specific file names don't matter but, well, since you broke your crystal ball, the specific one we are discussing is /home/engineering/SVP. Gee, did that help?? I've been doing this a while and would have said if it was a system folder. The exact command was... wait for it... ls. Can we both be done being smart-asses now?

dijetlo: I don't think it's a permissions or path issue because it's a new problem on an old machine, we do everything as root and I'm the one who would make path or permission changes/additions. This machine has been in production for years, to my knowledge nothing has been changed on it recently. It is possible something was changed without me knowing, but doubtful. We have close to 1000 of these in the client network and have never seen this particular piece of buggery before on this one or any of them. There would be no reason for a vendor to change anything on this machine and I know for a fact I did not, but I'll also concede that anything is possible.

I can't see that it could be a permissions issue: Nautilus should show everything, even lost+found, with a little cross if you're not even allowed to look at it.

I'd first try to see whether the problem lies in Nautilus or the files. Do they display with a different file manager, like pcman or gnome-commander?

i asked because they might have been all the "dot" folders and files
like .gconf or .local

those DO NOT normally show up

or

you might not have permission to see them if they are in a system folder or in a shared drive or a different users folders

and i asked for the "ls" command used
did you include the -a option?
the -l option ?
the -R recursive option ?
and so on ....