I was once in the situation that in the Dynamics AX Client the Manage Deployment Form (EPUpdate), found under "Administration | Setup | Internet | Enterprise Portal", did not list all Virtual Servers that were existing on IIS.
In this particular scenario the unlisted Virtual Servers in IIS were bound to a specific IP address, rather than "(All Unassigned)" which is this default. By chaging the ServerBinding back to "(All Unassigned)" the Virtual Servers started showing up on the Manage Deployment Form.
The Manage Depolyment Form is getting the list of Virtual Servers from a .NET Assembly shipped together with Dynamics AX and this Assembly uses the SharePoint Object Model to get all the Virtual Servers back. The only filtering takes place in the EPUpdate Form itself in the refreshServers method.