My initial exam shows that things should be doing what they’re supposed to. WP-O-Matic uses WordPress’s wp_insert_post which runs the appropriate hooks the Simple Tags uses. The only thing I can think is that if you’re using a cron job to pull posts, WordPress hooks aren’t run.
In laymen’s speak, Simple Tags doesn’t know it needs to add auto tags if WP-O-Matic is run via a cron job.
If it’s not run via a cron job, let me know, and I’ll look into it some more.