I'm really no wcf super guru so not sure if this is helpful or not, but one thing I remember about implementing the Authentication and Role services was that in order to get better control over the service endpoint to support multiple sites based on folder names where I needed to be able to have the folder name as part of the url for the service (and I did not want to have to hard code the service url in Web.config since it would change from installation to installation) I ended up implementing a custom ServiceHostFactory. So if you look in AuthenticationService.svc you'll see this:
<%@ ServiceHost Language="C#" Service="System.Web.ApplicationServices.AuthenticationService" Factory="mojoPortal.Web.mojoServiceHostFactory" %>
and mojoPortal.Web.mojoSeriviceHostFactory.cs can be found in the Web/Components folder.
really I have no idea if any of that has any bearing at all on your custom service or the problems you are having but thought maybe it was worth mentioning.