I don't know if this will help out but you could try it. I don't even use VNC. From a default screen on my client box (which has a bare minimum install of RH 9), I ssh to the server which has all the apps and programs. Both are on the same LAN. Upon connection and sign in, I just type "icewm" which gives me a de, but you can use the others too. Then I can run whatever I want on the server from the remote box, just as if I were at the server. It has always rebooted or shut down when I've commanded it to. This may be a way to see if the problem is somehow related to VNC.
When you try the shutdown or reboot commands from the console, are you attempting it outside of X, or pulling up a terminal on the server while in X? If while in X, I would also try just connecting to the server via ssh, then doing a shutdown or reboot command from the console. If it still hangs at reboot then there is something else going on. I've had boxes hang at shutdown and you have to manually power them off. I've never figured out what causes this.

thanks, i'll try using that. also i'm running g-nome and whenever i try and start file manager as a super user it appears then disappears immediately, i have this problem on my red hat box at home too. any ideas?

LOL! I have the same problems! If it's not being able to use Konqueror as su, then it's that damn CORBA error about 50 times when trying to run nautilus as regular user! Trust me, there is NO fix for the CORBA error! I've tried all of the "solutions", read all the bug reports and have asked on forums and nothing will fix it. It will remain the great unsolvable RH 9 problem.
Workaround:
 
Only use Nautilus as su:
 
nautilus --no-desktop
 
And only use konqueror as regular user.
 
Or another good option is to start using the Gentoo file manager.

this is turning into a nightmare... i tried to change the GUI to KDE instead of GNOME to try and fix the su in konqueror problem, then rebooted (got the telehousing to hard reset it) now it wont boot! the monkey i talked to knew nothing about linux so i couldnt get much info but basically i can log into the root account and use that fine, (but can only get console in VNC not full gui) but when i try and login to the normal account (the one it auto starts up to) it gives some error about "your session lasted under 10 seconds this could be installation error" or something or other. i assume this problem is to do with trying to switch to KDE, so i need a way of changing the GUI back to GNOME on the main account so that i can log into it and VNC properly... any ideas? i'm lost

try ctrl+alt+backspace...if i`m not wrong that`ll restart ur X-server. it`ll give u the login screen. on top upper left corner there is something written as "session" click that and from dropdown list select Gnome. put in the username and password and ur in.

oh right!! i'll try that too! thanks

shinymod, is this server on the same LAN with you, or is it off somewhere else beyond your modem? IF you and it are on the same LAN you can log in and contact the server via ssh, and it won't matter what GUI (DE) is up or even if the server is in X. You can still run your choice of DE as long as your client box has X installed, (which it surely does if you are using VNC), but you must do it from the Default session. Otherwise your server will detect a DE already running and it won't work.
Disregard all of this if your server is beyond your modem as the screen refresh would be agonizingly slow, even with a high speed internet connection.

unfortunately it isnt, it's in a the clara.net colo telehousing, but thanks anyway!

did you try setting up ssh and then reboot via the console.
 
Personally when i work remotely i use VNC, FTP, and SSH at all times.
 
If you are using windows, look up putty and OpenSSH... both of which are opensource and pretty much free.