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Just to be sure I'm getting this - Alert Central #2 is getting alerts from NPM, and you're getting email alerts from Alert Central #2 about NPM, but you're not seeing those alerts in the console for Alert Central #2?
One easy thing to do is toggle the views in the Alert Central alerts screen to see if maybe the time range/and or filters are showing a narrower view. You could switch from "My Alerts" to "All Alerts" and adjust the timeframe to be more broad.
This was actually a very simple one which was noticed after the alerts suddenly turning up after leaving the box alone for a few hours. It turned out the time was not syncing properly (time drift of circa 1 hour) and so were being filtered from view....