As soon as I added the feature .NET Framework 3.5.1 Features > WCF Activation > HTTP Activation, the IIS Server prerequisite in the Prereq Checker would say that IIS is either not running or was running without any authentication providers. I went into IIS Manager and tried toggling the Negotiate and NTLM providers around but it didn't seem to help. That did resolve an issue once where I had to remove/add the providers for the Prereq Checker to pick them up.
I was able to get all prerequisites to show green by running the commands in http://msdn.microsoft.com/en-us/library/hh169179(v=nav.70).aspx
- cd\Windows\Microsoft.NET\Framework64\v4.0.30319
- aspnet_regiis.exe -iru
- iisreset
I admit I haven't read the guides as throroughly as I should have (just playing with the product) and don't know IIS at all so this may be obvious to some but I wanted to throw it out there in case anyone else runs into it.