Let's consider a scenario wherein we have an FTP site hosted on an IIS Server and we are trying to setup the site to work in Active Directory (AD) Isolation mode. Now things should work just fine if we have the setup done properly. I have talked about general setup and common issues with FTP sites here.
This should ideally work fine for the domain users which are in same domain as IIS (Let's say Domain 1). We should know AD isolation mode is supported for domain users only and not local users. Now consider a scenario wherein you want to have FTP working for users from a different domain (Let's say Domain 2).This is not as simple as just running the iisftp.vbs script on the IIS server to set FTP Root and FTP directory properties for domain2 users.