The NI Web Application server is different for 32-bit and 64-bit web services. If you look on the web configuration for the NI application web server you can see you can set the port for each one individually - and of course only one can listen on a particular port at a time.
On my system, the 64-bit NI Application Web Server is actually disabled - so I doubt that trying to deploy a 64-bit web service would work for me.
LabVIEW Champion, CLA, CLED, CTD
(blog)