I suspect it is in fact related to recent changes in the community taxon calculation – however, not this most recent change but the previous one.
My guess is that whatever changes were made also involved redefining “disagreements” so that in some cases broader IDs are displayed as though they were disagreements. It is not related to whether the DQA is used or not – I checked a few of my observations that had a mixture of broader and finer IDs (but no disagreements) and it seems like under certain circumstances some of the IDs start being counted column 3 instead of in column 1.
It is also very very unintuitive – I really don’t understand what triggers this, but I assume it has something to do with community ID and observation ID being different.