When your colleague tries to make the change, be sure to look at the bottom left corner of the Editor window for any error messages.
One reason I can think of this would be if the Editor is unable to access the location that the preferences file is located. If it's read-only, or the user or application doesn't have sufficient privileges, then ideally you would see this mentioned down there. If you're not sure of the location of the Preferences file, you can find it in the "Help -> Session" dialog box.
The only other thing I can think of would be a custom script that is setting preferences. Usually that only happens at startup, but I can imagine someone writing a listener to check when preferences are modified, and change them back.
