Error in the webagent log file.
2008-10-20 15:43:45 -0600 - [9646/1078819584] - <Critical> - Logon page not configured for: CUSTOM_NETWORX.  CUSTOM_NETWORX was the name of the class entered for custom authentication for the server side custom authentication class

cleartrust.agent.custom_auth=CUSTOM_NETWORX

There is an error in the documentation that makes one believe the custom pages already defined in the webagent conf file are for this method of custom authentication. 
cleartrust.agent.login_form_location_custom=/cleartrust/ct_logon_custom_<%language%>.html
cleartrust.agent.login_error_user_location_custom=/cleartrust/ct_logon_failed_custom_<%language%>.html
cleartrust.agent.login_error_pw_location_custom=/cleartrust/ct_logon_failed_custom_<%language%>.html

These pages are for wax based custom authentivcation and not server side custom authentication.

For Server-Side Custom Authentication you must add the custom pages with a numerical suffix depending on how many server side auth types you have starting with custom1.  If you have two server side custom authentication types for example cleartrust.agent.custom_auth=MyAuth,SampleAuth

Then the following pages would be needed:
cleartrust.agent.login_form_location_custom1=/cleartrust/ct_logon_custom_<%language%>.html
cleartrust.agent.login_error_user_location_custom1=/cleartrust/ct_logon_failed_custom_<%language%>.html
cleartrust.agent.login_error_pw_location_custom1=/cleartrust/ct_logon_failed_custom_<%language%>.html
cleartrust.agent.login_form_location_custom2=/cleartrust/ct_logon_custom_<%language%>.html
cleartrust.agent.login_error_user_location_custom2=/cleartrust/ct_logon_failed_custom_<%language%>.html
cleartrust.agent.login_error_pw_location_custom2=/cleartrust/ct_logon_failed_custom_<%language%>.html

custom1 pages to support MyAuth and custom2 pages to support SampleAuth