Comments - explain result different in different versions
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I'm assuming you've tried ANALYZE TABLE from blog to ensure the statistics are up to date.
Without table structures, statistics, a full query or a full explain its hard to come to a definite conclusion.
There is a optimizer trace that shows detailed information as to how the query execution occurs.
EXPLAIN FORMAT=JSON offers a higher resolution, or ANALYZE FORMAT=JON for the run time execution of the query. Compare the estimates vs measured on the ANALYZE.
I'd relook at your composite indexes to see if they provide the most natural fit for your query.