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.
Best,
Joe