Ruby is supposed to be produced in higher quantities than Sapphire, as indicated by the settings:
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...but as seen in this image:
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...Sapphire Ore has a higher quantity than Ruby Ore.Possibly related, the gem sorting recipe (when unsorted ore is enabled) has the same issue, producing more Sapphire than Ruby.
Not sure where the source of this would be, since I couldn't find anything that would mess with those values.
Doesn't seem to be mod related, either, as starting a game with nothing but ores does the same thing.