I am having the same issue on Windows Server 2008 R2 Standard - clean build.
Every time I get to the deployment Assistant it shows and error and will not allow me to complete the deployment without going back and opting to NOT allow web publishing. I have uninstalled IIS and allowed the FMS installer to installer everything itself. No matter what I do, I cannot get web publishing to work.
Very frustrating!! Any suggestions welcome.
I had to call tech support to fix the issue. I had to remove my server from the domain and turn off my nic cards in order to install the software. But I was just on 2008 Standard. I wasn't using R2.
I ended up contacting FileMaker technical support. They said that if, during installation, I got a message saying port 80 and 443 were in use and did I want to disable them, then my system software was not standard. That is, the server should not by default have IIS already installed. Instead I should allow the installer to put IIS and other necessary software on the computer.
So I had our IT team create a fresh new server with no IIS preinstalled. I was then able to install without issue. I suspect that the version of IIS or some other system component was later than the FMS installer was expecting. Anyway, all seems very temperamental.