I solved this problem myself after not finding the answer in the forum, so thought I’d share what worked for me.
I’ve been using AST for months and it has worked well. I made several updates to the site recently, including adding a caching plugin (W3 Total Cache) and a security plugin. Not sure if those were the cause, but I noticed shortly thereafter that the AST tracking info was no longer appearing in any emails to customers. The plugin was working fine on the backend – tracking info was being stored with orders as usual. I had not made any changes to email templates that might have overridden what AST was doing.
The solution was to deactivate and delete the AST plugin and then reinstall / reactivate. Oddly, AST kept all its settings despite being deleted, so it was not much hassle. I also emptied the page cache via the cache plugin around the same time. The tracking info started going out with emails as usual.
Hope that helps others.