Just to ensure this was not related to any bug within our latest release of SmarterTrack 10 (10.1.5318 at the time of writing this post) I attempted to replicate this same behavior within my test environment.
When I changed over from using smartertrack.server.local to helpdesk.server.local by changing the base URL and issuing an IIS reset my survey's were sending out with the correct URL.
I'm unable to replicate the same behavior. However, there may be other factors in place here that could be causing the issue you are facing. Does the same behavior occur if you were to upgrade your environment to the latest release of SmarterTrack 10.1 ?
If the issue still occurs after an upgrade I would recommend opening a ticket with our support department and we should be able to get you squared away.
Technical Support Supervisor