thanks for the direction.

SQL Agent firing - Check

RS Processing Subscriptions - Check

SMTP delivering emails - Check (for many of the subscriptions)

Subscription invalid (I think this may be the issue with passwords not matching between applications)

I am checking into the last item. I have created new subscriptions today and they have been working. I also have created a history table for subscription events to see if there is any pattern.

I will update once I know more.