How did you remove the startup preference pane app? If you deleted the program without first turning the startup sound back on, that may be the reason the startup sound is still muted.
Reinstall the program (there's a new version available on the support web site) and turn the startup sound back on. Also, there's no reason to remove the program to restore the startup sound after it's been muted. The sound can be adjusted from completely off to on in volume steps.
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