How do I clear environment variables in 10.6

I am having some difficulty in configuring custom paths with my environment variable, environment.plist.  In setting up some of my software, I am trying to configure custom paths so that I can eventually store preferences on the server for all users to access the same tools.  I had this working up until last week, when I installed a second piece of software, that modified my environment.plist file, which now doesn't work at all.
My original environment.plist file, which is located in ~/MacOSX, was as follows:
<plist version="1.0">
  <dict>
    <key>NUKE_PATH</key>
    <string>/Users/jamesdavidson/Documents/Nuke_Gizmos/Nuke</string>
    <key>OFX_PLUGIN_PATH</key>
    <string>/Users/jamesdavidson/Documents/Nuke_Gizmos/OFX</string>
  </dict>
</plist>
Which worked just fine.  It was then changed to:
<plist version="1.0">
  <dict>
    <key>NUKE_PATH</key>
    <string>/Users/jamesdavidson/Documents/Nuke_Gizmos/Nuke</string>
    <key>OFX_PLUGIN_PATH</key>
    <string>/Users/jamesdavidson/Documents/Nuke_Gizmos/OFX</string>
    <key>PATH</key>
    <string>/bin:/sbin:/usr/bin:/usr/sbin:/usr/libexec:/Applications/Deadline/Resou rces/bin</string>
  </dict>
</plist>
and now, the only variable that shows up is PATH.  I edited the file back to the original, without the PATH variable, restarted my machine, and yet my Variables did not change...  Is there somewhere else that I should be looking?  Some other file?   this is what I get from terminal:
$ echo $NUKE_PATH
$ echo $OFX_PLUGIN_PATH
$ echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Applications/Deadline /Resources/bin
And this even after deleting my environment.plist file.  Any help would be appreciated.
Thanks,
James

I hope you made a typo in your post and meant ~/.MacOSX.  You typed ~/MacOSX, i.e., without the leading dot.
At any rate $PATH is a predefined shell variable so I suspect you cannot define that one with this environment.plist mechanism.  The "proper" way to set up such things is with a  ~/.bash_profile, ~/.bash_login, ~/.profile, or IMO, best of all. ~/.bashrc.  These are scripts the shell looks for during launch (somewhat depending on whether it's a login shell or not -- see the bash reference manual).
If bash is executed interactively it will also first look for /etc/profile.  And it will cause a $PATH variable to be created.  So that is probably the definition you are seeing all the time until you create an appropriate startup script of your own (e.g., ~/.bashrc) to override or modifiy the existing $PATH variable.
Note, I may have paraphrased a lttile too much so see section 6.2 Bash Startup Files in the bash reference documentation for the complete proper description of the order these files are used.  If you have the developer tools installed look for bashref.html.  Otherwise it's online here.
Finally, if you look at /etc/profile you will see it attempting to execute /usr/libexec/path_helper -s.  Try that in terminal and see if that isn't the $PATH definition you are currently seeing.

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