From MozillaZine Knowledge Base

This article was written for Thunderbird but also applies to Mozilla Suite / SeaMonkey (though some menu sequences may differ).

Some applications make SimpleMAPI calls to check for new messages. This will start the default email client, if its not already running. If the application was automatically started by Windows and Thunderbird was configured as the default email client Thunderbird would automatically launch when Windows boots.

You can prevent this by configuring Thunderbird not to be the default mail client. If you can identify what software is checking for new mail on startup you could also try disabling that feature.

Google's Picasa software, some BIOS's, a helper application associated with the IBM Rapid Access III Keyboard, and a Active Desktop theme for a IBM Thinkpad have been known to do this.