I have very odd situation, all but one realtime alert are working fine. One alert which flags up the 404s works for a few minutes after splunk restart and then it stops sending emails. Neither python.log nor scheduler.log shows any sort of errors. It looks like an alert would never be triggered, however when I open the search result i can observer that search actually works.
This doesn't seem to be the same issue you are having but I had a similar problem after upgrading to 6.1.1 where some alerts wouldn't fire. In my case it also seemed to be related to the account that owned the search.
My situation seemed to be known issue SPL-84357. The workaround was to add a session timeout line to server.conf (sessionTimeout = 30d). After making the change and restarting the alerts fired as expected.
I've included the links I found most helpful here: