When we try to use the web administration interface (or any function using WA.EXE) the browser tries to open the executable WA.EXE instead of the web server executing it.

This means that you do not have the access permissions for WA.EXE set so that it can be executed. You need to open the IIS management console and set the access permissions properly so that the file will be executed rather than read. You may also need to enable the CGI-exe handler mapping for your website in the IIS Manager (it comes disabled by default).  Also ensure that WA.EXE has the correct NTFS execute permission.