On activating trace in SQL Monitor we immediately set trace running on the relevant monitored server. When an alert is raised that supports trace (going from memory this would be Deadlocks, Long-running Query, Job Failed, Blocked Process and Error Log entries), we read the trace files and transfer data for the relevent process and time period into our data repository. The recently raised alert should display this trace data although not always straight away. If there's a lot of trace data in the time period that the alert was raised it takes a while to transfer so there could potentially be a couple of minutes lag before the trace data appears. I believe that you'd need to reopen the alert to get the trace to appear.
So do you see the call to the stored procedure but not the code in the stored procedure itself?