Permanently Change Environment Variables in Windows
Sounds like the AD profile on the domain is overwriting the user defined variables. I see your screenshot says you are connected to the eait.org.edu.au domain. That will be the root of your issue. Just to include some details here that I spotted elsewhere, that may be of help to you:
HOMEDRIVE, HOMEPATH & HOMESHARE are set and updated via Active Directory. HOMEDRIVE & HOMEPATH are set even without a home drive set on the account; however they will be overridden by any user account properties set in AD.
Also see these KB articles:
http://support.microsoft.com/kb/841343
http://support.microsoft.com/kb/237566
http://support.microsoft.com/kb/101507
On a side-note for another way around the issue:
-I have in the past created a new instance of the windows command-line shell executable that automatically runs a custom script, so everytime you launch the shell, the environment variable could be overriden.
-To do that you could just put the code you posted to change the environment variable into a batch script, stored wherever you like, then edit the shortcut(s) used to launch the shell by going to properties > then alter the Target box: %SystemRoot%\system32\cmd.exe /K "C:\Documents and Settings\Administrator\My Documents\customshellscript.cmd" (Obviously the part of the path after /K is the location of your custom script)
This way, if you are using openSSH over the console anyway, it will always have the homedrive set correctly.
Nowhere does it mention a dependency between the HOMEDRIVE value and the HOMEDIRECTORY value, what was happening (I think) is that it was failing to map the home directory to the HOMEDRIVE and therefore defaulting back to a safe value (C:)
I wrote a script to update the local AD, replace the values in [] with your values. Copy and paste into a .vbs file and double click on it to run it.
Set objUser = GetObject("WinNT://[COMPUTERNAME]/[USERNAME],user")
objUser.homeDirDrive = "H:"
objUser.HomeDirectory = "[URNPATH]"
objUser.SetInfo
e.g.
Set objUser = GetObject("WinNT://UQBDART-2328/BEN,user")
objUser.homeDirDrive = "H:"
objUser.HomeDirectory = "\\SERVER\SHARE"
objUser.SetInfo
run this, reboot and test. It worked for me.
Changing those environment variable's values is not "supported", at least it will not work as you expect because Windows changes them back.
According to this Microsoft knowledge base article (KB841343), you should use policies, if you need to change these settings. The article also contains links for how to do that (but personally, I never tried). Note that the article was originally written for Windows 2000, but I would strongly suspect, that it is still valid for current Windows versions.