Well I'm not too sure how familiar you are with the registry.
But if you look at the columns in the msconfig utilties startup tab , you
can find which key that app might have used to start-up.
Most likely HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
OR
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run
If you are certain that the application is no longer in use then you can
nail it in one of the above keys.
I'd also suggest having a look at your program files folder , if you do not
plan on reinstalling the package , you can free up some clutter here too.
I'm not sure of any apps that can pick up orphan reg-keys like these , I'm
not fond of the damage most regitry cleaning tools cause , but maybe I'm the
only one.