While experimenting with how to manage civilian economy, I ran a year in 1-day increments, and now I'm running a year in 5-day increments, versus my usually 30-day increment when nothing interesting is happening. I've noticed that even with auto turns checked, the processing stops every 5 or 10 days. Nothing shows up in my filtered player event log, but checking the SM view shows some events. It appears that only some of the filtered events are causing the auto turns to stop processing. For example, two New Officer events and an Exceptional New Officer event didn't cause Auto Turns to stop, but two New Officer events, a Civilian Construction event, and a Civilian Mining Colony event did cause the auto turns to stop.
I think it would be better if the auto turns didn't stop on events that I've filtered out.
EDIT: Further testing shows that either Civilian Construction or Civilian Mining Colony events happening, even when both are filtered out of the player view, cause Auto Turns to stop. Tried this with SM mode on and off, with the same results.
EDIT 2: Mineral Exhausted (when filtered) also appears to stop Auto Turns.
EDIT 3: Ship Scrapped (when filtered) also stops Auto Turns.