In #8861 we introduced a mechanism to cache some of the subqueries done in Piwik archiving process. These speedups could technically bring up to 50% speed improvement in some particular cases. It is un-expected that the cache should make the execution time slower, but it could occur in some cases.

[General]
; whether to enable subquery cache for Custom Segment archiving queries
enable_segments_subquery_cache = 1
; Any segment subquery that matches more than segments_subquery_cache_limit IDs will not be cached,
; and the original subquery executed instead.
segments_subquery_cache_limit  = 100000
; TTL: Time to live for cache files, in seconds. Default to 60 minutes
segments_subquery_cache_ttl  = 3600

Steps:

• Verify the limit setting is set to safe value (was initially set to 100,000)
• Enable by default for all users in global.ini.php