Is there any difference in the way stubs are generated for secure and non-secure endpoints?
I created stubs using secure endpint wsdl, but it is giving me "Invalid username password" when I invoke the service from a client.
What should I do if it is a secure ?

change your endpoint https URL to include fully qualified domain name (fqdn) like
https://sth.domain.com rather than ip address. It may be looking for valid SSL cert of the endpoint.