On a recent problem, I was installing an Application Pool, Website and Web Application to IIS and no matter what I did, it would not install correctly.
I had been through everything, the Help, I had examined the IIS properties for each item a number of times, done research in the forums and still nothing worked.
Then I remembered that this had happened to me twice before. In those times, the problem was solved by clearing out everything in the IIS view of the InstallShield project and recreating everything. So, I did that this time and it fixed the problem.
If you have a lot of items installed to IIS, this is not an ideal option, but it is one option that works sometimes. I’m not sure if something gets corrupted in the IIS view’s information, but recreating makes it work.
Test it out the next time nothing else works.