When I fired up the GECK for the first time, it remembered my old screen positioning, and the GECK was so far to the right as to be unreachable, out in virtual space where my old second monitor had been.
To fix this (Windows XP) I went to this file:
C:\Documents and Settings\Me\My Documents\My Games\Fallout3\GECKPrefs.ini
And within that file, I found this:
Object Window X=2094Object Window Y=284Object Window W=933Object Window H=498Object Tree X=0Object Tree Y=28Object Tree W=288Object Tree H=443Object List X=293Object List Y=0Object List W=632Object List H=471Cell View X=2490Cell View Y=233Cell View W=574Cell View H=530Garden of Eden Creation Kit X=2038Garden of Eden Creation Kit Y=83Garden of Eden Creation Kit W=1074Garden of Eden Creation Kit H=810Render Window X=2404Render Window Y=583Render Window W=395Render Window H=234
and I edited it to say this
Object Window X=0Object Window Y=0Object Window W=933Object Window H=498Object Tree X=0Object Tree Y=28Object Tree W=288Object Tree H=443Object List X=293Object List Y=0Object List W=632Object List H=471Cell View X=0Cell View Y=0Cell View W=574Cell View H=530Garden of Eden Creation Kit X=0Garden of Eden Creation Kit Y=0Garden of Eden Creation Kit W=1074Garden of Eden Creation Kit H=810Render Window X=0Render Window Y=0Render Window W=395Render Window H=234
and then when I started GECK , all of the windows were reachable again.