oh. ok says it is running... that's different issue then.
ok let's try to isolate the problem.
1) so if you launch the config tool from the tray tool, it does show as running in the config dialog.
that's good, at least the apps are talking.
2) now when you added your rule, how exactly did you add it?
did you add it manually from the configuration tab by right clicking and selecting "add rule", or did you add it by clicking on the Processes tab, finding the app and selecting "Ignore".
3) either way:
when you close the config tool and reopen it (always open config tool using tray tool), is your rule still there?
4) now before we get to the subtleties of disabling and enabling and obeying rule changes -
can you check if you exit the tray program completely, and restart it, is it now obeying the ignore rule?
once we know the answers to these we will know a lot more about the cause.