This is probably due to the Default-Web-Path entry in the ar.cfg file. This is a hard coded URL of the Midtier uses for emails/alerts by AR System processes.
Single Sign On for BMC AR System
I found the answer but had to confirm with positive results before posting. Well I just now had the problem again on a test server and fixed as below.
I updated Midtier/WEB-INF/viewer.properties. There is a parameter in there called "base_url" which is commented out by default. I changed it to:
Hope this helps!