I can't answer that question in detail, but I can say that on Windows 2003 servers under x64 you must explicitly set up IIS to Allow Web Service Extensions for ASP xxxxx (32) applications. In a console window, type:
cscript %SYSTEMDRIVE%\adminscripts\adsutil.vbs SET W3SVC/AppPools/Enable32bitAppOnWin64 1
Then proceed with the following steps:
- Open IIS; Web Service Extensions
- Click on Allow All Web Service extensions for a specific application
- Choose ASP Net vX.Xxxxx (32)
- Click OK
- In a command window type IISRESET
This should help get your application back online! 
Other references include:
http://msdn.microsoft.com/en-us/library/k6h9cz8h(VS.80).aspx
http://www.iisadmin.co.uk/?p=15#more-15