If you're using the same install, then it should be the same folder and shouldn't matter.
If it's the light blue dots and the light blue regions that aren't showing then it's not an issue with EQ2MAP, as those are acutally POIs provided by the game (by SOE). Did they disappear, or are you just not getting them with new quests? Unfortunately, not all quests have those, mainly just DoV and later and the "Golden Path" zones.
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