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Obvious questions are:
Was the crawler completely finished and not just done fetching?
Was the index optimizer running at this time? This could definitely lead to these strange results.
Behavior definitely sounds like user was not logged in. I assume you saw the user ID in the top right of search indicating you are logged in?
We are running 188.8.131.52.0 and don't have those issues.
I've actually submitted an SR for this.
But yes, the crawl was complete. At least according to the Schedules page on the admin site. And no, I was not rebuilding the index at that time. I have that set to go only on Sunday afternoons.
We changed this setting:
SES Admin UI->Global Settings->Query Configuration->Security Filter Lifespan (minitue) = 0
And it may have helped. Still not entirely sure since the problem is intermittent and we have not been able to determine a cause.