Does the program have a "run at startup" option in it's settings? If so, turn it off. If it's running from your startup folder, remove the shortcut from the startup folder. If it's runing as a service, go into the service and set it's startup property from automatic to disabled or manual.
Autoruns may also be able to help you.http://technet.microsoft.com/en-us/sysinternals/bb963902