Gems are replaced with lower quality ones

Seems like the gem filter is a bit too aggressive. Example: My character has blue gems in all sockets, but with the setting “Uncommon” they are replaced with green ones, altough the existing blue ones give a higher score.

Have you tried re-importing, after gemming… to secure the new baseline?

You mean from the addon? Yes, I do that multiple times a day for best in bags.