We are using the Extended Email Plugin for our alerts and all works fine but the filter for incidents from a particular Agent or Agent Group doesn't work.
We test this with one simple alert on Exception count, if we configure the Extended Email Plugin without Agent or Agent Group restrictions all works fine but if we put one restriction in Agents or in AgentsGroup the notification email is never sent.
I assume JavaApplication_Monitoring is a single agent name correct?
One thing I thought of to check in your test is to make sure the measure you're using in the incident is set to create a measure per agent otherwise the context won't be in the measure to be able to filter by agent.
I just did a quick check and if you create a new measure for exceptions count it is only created per application by default.