I remember an issue like this one - go into the parent application's Preferences. If they were at all nice about it, there's an option in there to enable/disable the startup item.
BTW, is it so bad to have it start up? I mean, if it took an extra ten seconds to log in or presented an annoying window, I'd disable it myself. There are some programs, like Virex, that have start-on-login programs that are completely transparent. i believe the Virex headless program keeps an eye on programs in memory, and the scanner's one keeps a lookout for whether or not the scanner is connected or on. For instance, if your scanner has a one-touch scan feature, and you would care to use it, then this backghround program is a boon.