You probably have 2 installs of EQ2, with the auto-updater not pointing to the one you're actually using.
Launch the game patcher as you normally would to play the game, then click the little hammer and wrench icon in the bottom left, just above the gold progress bar. Then click open game directory -- this will show you the directory on your computer that you're actually playing the game from.
Now open the EQ2MAP updater and go to options. Under "Everquest 2" in the top-most box should be a path that leads to the same folder you found above. If it doesn't, click the browse button next to it and navigate your way to that folder to set the location properly.
To get it to use the patcher properly (and not give you that error about launching manually), repeat the process with the second browse box, only this time selecting Launchpad.exe in that same folder you found above.
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