Hello Andy, I've ran across similar problems while trying to install a new instance of SQL Server 2005 Express Edition with Advanced Services on a Windows Server 2003 machine that already had an instance of SQL Server 2005 Standard.
This system was also the functioning as the companies production web server which had SSL certificates installed (in IIS6). After talking to one my coworkers, he said the only way around this is to uninstall ALL of the SSL certificates in IIS, install SQL Server and then reinstall ALL of the SSL certificates. :w00t:
Since this their only production web server and I don't know how to install/uninstall SSL certificates in IIS, I was fortunate enough to have another server that I could install SQL on.
My coworker said that this is the solution that he got from Microsoft too... :ermm: I don't remember the details of the conversation, but he said that it had something do with the services trying to connect to the computer, but the SSL was confusing it.
I know the solution is kind of a pain, but I hope this helps. 🙂