From a little Googling it seems like authentication information is only passed to Apache when requested. Since your Windchill logon appears different than the Windows logon, the information being requested will be specific to Windchill, not Windows. Not sure if it's possible or not, but you'd probably have to configure double authentication. Basically some type of hidden single sign on using the windows credentials and then the normal LDAP login for Windchill.
Here are some things on NTLM authentication:
http://www.apachelounge.com/viewtopic.php?p=25073
http://board.phpbuilder.com/showthread.php?10377804-RESOLVED-AUTH_USER-Apache-in-Windows-Domain