First off, EQ2MAP has absolutely *nothing* to do with the way /waypoint works. Normally putting in a properly formatted waypoint will tell you a direction to go (i.e. it's to the North and above you) and only when you are close does it make a trail. Yes, it's buggy. No, it's not EQ2MAP's fault.
Next -- selected the POI should cause it to blink/glow on the map. In a heavily populated map it can be easy to miss. To see this in action, find a POI you can see on the map, look at it very closely and then select it (from the find menu). It should begin to blink/glow.
Oh, and another alternative is to find the POI on the eq2map website itself. When you look at the individual POI there, it will be the *only* POI displayed on the map.
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