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The campaign ran great.
Ran great for whom? For you or for Google? Your objectives (max conversion @ high ROI) are not necessarily in-sync with Google's objectives (high CTR @ high CPC). The Quality Score judges according to G's objectives.
IMO, if you have a stellar CTR but a low CPC, you are even more at risk than if you had a low CTR because you are pulling clicks away from high bidders. Stark contrast to the good old days, when CTR alone determined what was quality.
Not really sure why the QS would judge "batches" of KWs differently, though. That is odd.