If you right click on the map and hit Filter POIs, make sure they're all checked - it's possible to turn off those POIs I believe just like you can filter regular POIs.
I'm not sure about the 2 update folders. Could you post a more complete tree of where those two folders are? IE, do you have \Everquest 2\UI\LP_region_En-US\eq2map or is it some other arrangement? I only use the US region so I'm not sure how its set up. It may be that the game keeps two separate UI folders for different regions in which case you'd need to update both. How to do that with the updater would depend on how the folders are arranged.
Assuming there are two separate folders, there are ways to link them in windows so that you only have one. How to do that depends on your comfort level and familiarity with computers.
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