I have two Windows 2003 x64 R2 IIS boxes that are ostensibly setup the same way.
But for whatever reason, one of them has a W3WP.exe process for each application pool and the other one does not.
What could be the reason?
Can you verify if all the applications/Web Sites on the other server is accessed as well. w3wp.exe process won't be created unless the application is accessed. Probably the first server is taking all the requests and no requests are handled by the other server.
Try browsing iisstart.htm page which is there in Default Web Site and you should see a w3wp.exe process created.