Hrmm... yah I recall something similar. Do the following...
Look in your Everquest II directory for a file named as follows...
YOURSERVER_YOURCHARACTER_eq2_uisettings.xml
Make sure its the XML file and not the INI file of the same name.
Copy the file to your desktop so you have a backup if something goes wrong in editing.
Open the original in Notepad (Make sure Word Wrap is unchecked)
Search for
That should bring you to the extra map window entry if present. Now delete everything from that opening Window tag to next closing window tag
Code:
<window Name="Map2_clone_2" ...
<Properties ...
<MapSettings ...
etc...
</Properties ...
</window>
Save the file and launch EQ2 to see if the problem is solved.
If that fails to solve the problem, repeat the above... this time delete all Map2_clone window entries. This will likely move your map windows, but should force the EQ2 client to rewrite the correct settings.