When using a Custom Web Site with System Center Configuration Manager 2007 SP1 or SP2 and manually installing Secondary Sites, the Secondary Site installation may not update the following properties in the Sitectrl.ct0 file on the Secondary Site:
This property has no entry for the website name on the affected sites: PROPERTY <IISWebSiteName><><><1>
The DisabledPortList property is missing all together on the affected sites.
When this issue occurs, all roles with IIS functionality have their respective Virtual Directories created under the SMSWEB website as expected except for the Distribution Point. When you deploy the first package to the DP on one of the affected Secondary Sites, the Virtual Directories get created under the Default Website instead of the SMSWEB Custom Web Site as expected.
Also, in some instances the custom ports that are configured for the custom web site get bound to the Default Web Site as well, causing the site to not start. This can also cause the Management Point to not function.
When selecting the 'Use Custom Web Site' option on the 'Ports' tab of the site properties dialog, the Administration Console does not apply the option to any child secondary sites. This is caused by an issue in ConfigMgr 2007 that can occur when the Secondary Site is installed.
To resolve this issue, use the SDK to modify the Sitecrtl.ct0 file on the secondary site.