Heh, wanted to spam a POI thread as well.
I was in The Down Below yesterday sneaking into Qeynos and wanted to check the map for the zone-in to SQ. To my surprise none of the zone-locs where showing (I had some other POIs though).
I checked the map online on the website and all information is still there. Comparing it to what I was seeing ingame showed that I was actually missing a whole lot of other POIs as well.
Possibly there is a problem with your proggy that creates the XMLs? (didn't check the XML to see whether the POIs where in there at all and just not visible or whether they missing completely).
And yes, EQ2map was up to date.