After installing new software using the package manager, xfce4-appfinder does not list the new software. This is not good because I remove start menu from panel (I think is not needed) and start programs with xfce4-appfinder (Alt+F3). Please make the appfinder update its list on startup, or include an update button in the settings.
I can't reproduce on Arch Linux. I just installed filezilla via pacman and appfinder is able to find it without any trouble, no matter if it's running in background or not. Please confirm if this bug still affects you, if so, tell which distro you're using, which package you're installing and what you have to do to appfinder list the app.
Closing, reopen if this is still an issue.