Pretty simple. Open a case. Reply to an email associated with the case, from CRM. Email goes out to customer. Customer replies. Reply goes to CSR. Tracking tag remains. Activity never appears in CRM/Case. The CSR can respond to it fine. Tag remains in place the whole time.
Settings has tracking enabled. Both tag and smart matching. Just never happens. CSR email is configured (can send, afterall).
What might be the issue?