I am having the same issue. I have a server farm w/ a stand alone sql server. I'm successfully running sharepoint. The server name was changed when sql was installed from "server002" to "RTDB1".
I did see SERVER002 in SQL studio. I ran the query to change to RTDB1. restarted the server. Studio now shows RTDB1, but I still get the error when installing Dynamics.
I have noticed that SERVER002 shows up in the main IIS page under connections. I have not seen any solution for fixing that, yet.
Brison