Does it say "ADMINISTRATOR" (in all caps) in the Opus window titlebar?
Running the whole dopus.exe process elevated (rather than individual windows via Opus's Admin Mode) could block receipt of the WM_SETTINGCHANGE message (assuming UAC is enabled on the account; if not then it doesn't matter).
Do you see the same issue if you launch the command prompt via Explorer or something else? The issue could be that the prompt isn't using the same user/context as the env-vars being edited.
When you exit Opus, are you fully exiting (via File / Exit Directory Opus), or just closing the window? If the env-var change isn't seen even through a full exit then the problem can't be related to Opus or WM_SETTINGCHANGE, since it isn't propagating to new processes either. (Unless the process from which you are launching Opus has the same problem, but presumably that is part of the system, e.g. the taskbar.)