Have you by chance added an onApplicationStart method to your application.cfc that is overriding the inherited one from coldbox/system/coldbox.cfc. That runs a loadColdBox() method that starts up ColdBox. You would need to call super.onApplicationStart() to ensure that functionality is preserved.
Thanks!
~Brad
ColdBox Platform Evangelist
Ortus Solutions, Corp
E-mail: brad@coldbox.org
ColdBox Platform: http://www.coldbox.org
Blog: http://www.codersrevolution.com