Figured it out, I misinterpreted how things were intended to work. My problem was I was pulling the subject name straight from the email trigger so the job only ran for the email that triggered the job but since multiple emails matched the trigger condition they all got marked as read. I was thinking it would scan the inbox, find the first matching email, mark just that one as read, run through the tasks, and then 60 seconds later repeat the process on the next email that matched.
I'm going to modify it to instead just use the trigger to trigger the job and then adding a "email - get messages" as the first step to obtain all of the subject lines and then iterating that tasks on that list.
Thanks.