The alert search is scheduled to run every 5 min and send us an alarm when it sees no events. So, what going on is between 2-3 am CT - Splunk starts sending us false alarms because it didn't see any events in the search. But when we looked back the events in that time frame we can find events there.
This brings us to a conclusion that either the events are getting delayed to reach splunk or the alert search itself cannot see those events (this can be very strange and don't know how).
We checked for the thruput limit configured for this splunk instance and found the value is set to 512 KBps. We are not sure if this is cause of the problem. We are still researching, but if anyone has seen this or knows about it, please do let us know to fix the issue.
We also saw issues like this and changed our searches that were running every 5 minutes to not look at the _time field but instead at the _indextime field by creating a macro called alert_time that takes one parameter($minutes$) and is defined as: _index_earliest=-$minutes$m _index_latest=now, and then we set the searches to look back over maybe the previous hour but specify alert_time(5) inline in the search.
This worked really well for us until we moved to a multisite approach with two indexer clusters that replicate between the sites. We have subsequently needed to delay our searches by creating a macro called alert_time_shifted that is defined as: _index_earliest=-10m _index_latest=-5m.
You can play around with the times here and see what works well for your environment to avoid hitting the strange 2am-3am delays.
First, refrain from sharing sensitive information like your instance URL. (I've masked it). The delay could be a indexer level as well if there are too much data coming their way. We generally recommend allowing few minutes of delay in the search's time range to account for this indexing delay. So my question would be, what's the time range you're using? You're running it every 5 mins so my suggestion would be use -5m@m (start time) to -10m@m (End time) as time range (assuming you were looking at 5 mins worth of data).