Two things for our 10.2 installation: httpd.conf and wt.properties.
In httpd.conf, set ServerName to [VM]:[port]. For example:
ServerName vm-windchill.localdomain:8080
For wt.properties, use the command:
xconfmanager -s wt.server.codebase=$(wt.webserver.protocol)://[VM]:$(wt.webserver.port)/$(wt.webapp.name)
For example:
xconfmanager -s wt.server.codebase=$(wt.webserver.protocol)://vm-windchill.localdomain:$(wt.webserver.port)/$(wt.webapp.name)
You might need to escape special characters. This also assumes wt.webserver.port=8080.
I think Lori is right, this is probably an Apache issue. But once you get that taken care of, Windchill might still be confused if you don't set the property in wt.properties. If you're lucky and Windchill doesn't get confused after setting the property, then at least you'll probably notice the VM name automatically removed from the URL in the address bar, and reverting back to the hostname.
This was our experience anyway...