With NCE 3.0 we use many NoteCaddy stats throughout their HUDs, Popups, and Badges. The NoteCaddy stats have filters which are independent from HM2 filters. This means that your HM2 filter settings don’t apply to NoteCaddy stats and vice versa.
You will want to make sure your NoteCaddy filters match up with your HM2 filters. This article is very helpful to show you how to do that: http://wiki.assaultware.com/Understanding-why-NoteCaddy-stat-values-may-not-match-HM2-stat-values.ashx