Feeds Module stops Automated runs after Alias is added

We are using the Drupal Feeds Module (https://www.drupal.org/project/feeds) on many sites in Aegir and it is working wonderfully on most sites. Once we add an additional alias (besides the www. one) the automated process stops running. From what we can tell this isn't an issue with the module it is something with what all is changed once an alias is added. We can manually import everything, but as we keep adding aliases our list of sites to manually import is growing rapidly.

Any help would be greatly appreciated.