OK - similar issue here - I used the Enterprise Builder wizard and it set up both Portal and Server Web Adaptor using the "default" IIS site, I didn't get the options you do when you set the Web Adaptor up on its own - I had already started using the default site for my internal JS mapping site.
Ideally I want the Web Adaptors to be on their own IIS site, I thought I could just rename the IIS site it had used (I had renamed it to be "emap" the name of our internal system) - the I could move my mapping site to another IIS site - not too big an issue as we are still in dev for this server.
Yet renaming the IIS site broke the adaptors - somewhere it must store the IIS site name. Any ideas?
Cheers
ACM