I can't access Nexus now, but I bet your problem is not with the map markers as such, but with a mod that alters the map and its dimensions.
EDIT: As I thought...you need to make sure the new map mod loads as late as possible, otherwise the game will use the new map graphics, but use vanilla dimensions (or world co-ordinates) resulting in the map markers being off.
At a guess, I'd say you are using a map that includes Stirk, and not using the MergedMaps.esp, or not using a map that includes Stirk and are using MergedMaps.esp.
Edit:Moved Mergedmaps.esp all the way to the bottom, it was second to last.
Didn't work.
Are you absolutely sure that the map in-game is the map that comes with Merged Maps? If you are using Stirk it's possible Stirk's map is used instead, if Stirk.esp is tagged with Import Graphics.
I turned off Stirk once just to see and it was the same map.
Also I didn't add the stirk map to my data folder I followed the readme instructions for not copying the map. It cna be found in my Isle Of Stirk Thread.