Or there aren't objective standards for what "low, medium, and high confidence" actually mean, thereby allowing one agency to look at the evidence and say it's of low confidence and another to look at the same data and say it's moderate confidence.
Or they are coming to different conclusions given the same ambiguous/incomplete information. It could simply be disagreement, or just lack of a standard metric here to compare notes easily.
I read that they did massively increase sharing after 9/11, but there was a reassessment after the Manning leaks. Manning had access to way more information than someone at their level needed for their job, and they concluded this came about from going a bit too far on the post 9/11 sharing and so they dialed it back a bit.