The issue is that the old info is being retained between uploads, since that's the default functionality. You need to remove all the tags for all the contacts you're trying to update so that their tag field is 100% empty. Then, on your next reupload post-tag purge, when you include the desired tags alongside the contacts, it'll actually add to them.
If you continue to have issues, I'd strongly advise calling our general support so they can provide live assistance, and screensharing if necessary.
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