this should be possible. Each character that you've logged into has a subdirectory and a Prefs_2.xml file stored inside it on your hard drive.
Inside that there's the following:
Code:
<Archive name="MapWindowConfig">
<Point name="window_pos" value="Point(700.000000,355.000000)" />
<Point name="window_size" value="Point(512.000000,400.000000)" />
<Float name="world_map_scale" value="0.000000" />
<Float name="region_map_scale" value="0.000000" />
<Point name="region_map_scroll_offset" value="Point(0.000000,-112.916504)" />
<Point name="world_map_scroll_offset" value="Point(0.000000,0.000000)" />
<Bool name="ShowWorldmap" value="false" />
<Bool name="ShowLegend" value="false" />
<Bool name="ShowBottomHeader" value="true" />
</Archive>
I'm assuming your "window_pos" co-ordinates are over 1000 each... setting them to under 500 each should solve your problem, if you edit them while the game is running so that they don't get overwritten immediately after character login.