May 04, 2012 09:29 AM|Steven Cheng - MSFT|LINK
One thing mentioned in the following document is that when using ASP.NET compatiblity mode for WCF service hosted in IIS 7, we cannot expose non-HTTP protocol based WCF endpoints in the service. Is there any non-http endpoint in your case?
#WCF Services and ASP.NET
BTw, if there is error occuring when the IIS application pool trys to start, you can also check the windows eventlog (under Applications category) to see if there is any related errors .