The Script Editor is written for MEL (Maya Embedded Langauge) and also python since version 8.

Try:
https://www.3dbuzz.com/vbforum/showthread.php?t=128327

I am not a MEL scripter but enter each of these in the Script Editor or copy them over your current windowPrefs.mel file (found in C:\Documents and Settings\<username>\Maya\<maya version>\prefs :

windowPref -topLeftCorner 225 150 -widthHeight 250 400 -parentMain true outlinerPanel1Window;
windowPref -topLeftCorner 250 200 -widthHeight 700 400 -parentMain true hyperGraphPanel1Window;
windowPref -topLeftCorner 250 200 -widthHeight 660 400 -parentMain true graphEditor1Window;
windowPref -topLeftCorner 250 200 -widthHeight 660 400 -parentMain true dopeSheetPanel1Window;
windowPref -topLeftCorner 250 200 -widthHeight 660 400 -parentMain true clipEditorPanel1Window;
windowPref -topLeftCorner 250 200 -widthHeight 560 430 -parentMain true multiListerPanel1Window;
windowPref -topLeftCorner 250 200 -widthHeight 524 470 -parentMain true devicePanel1Window;
windowPref -topLeftCorner 19 1288 -widthHeight 747 740 -parentMain true hyperShadePanel1Window;
windowPref -topLeftCorner 250 200 -widthHeight 700 400 -parentMain true dynPaintScriptedPanelWindow;
windowPref -topLeftCorner 250 200 -widthHeight 550 562 -parentMain true blindDataEditor1Window;
windowPref -topLeftCorner 341 426 -widthHeight 540 505 -parentMain true learningMoviesLaunchWnd;
windowPref -topLeftCorner 720 750 -widthHeight 530 276 -parentMain true CommandWindow;
windowPref -topLeftCorner 0 0 -widthHeight 1280 996 -parentMain false MayaWindow;
windowPref -topLeftCorner 279 868 -widthHeight 278 500 -parentMain true ColorEditor;
windowPref -topLeftCorner 17 1284 -widthHeight 422 670 -parentMain true unifiedRenderGlobalsWindow;
windowPref -topLeftCorner 384 1799 -widthHeight 680 600 -parentMain true renderViewWindow;
windowPref -topLeftCorner 210 390 -widthHeight 630 450 -parentMain true PreferencesWindow;
windowPref -topLeftCorner 175 134 -widthHeight 441 650 -parentMain true AEWindow;
windowPref -topLeftCorner 14 1302 -widthHeight 913 949 -parentMain true polyTexturePlacementPanel1Window;
windowPref -topLeftCorner 341 426 -widthHeight 525 350 -parentMain true OptionBoxWindow;
windowPref -topLeftCorner 341 426 -widthHeight 376 349 -parentMain true shelfEditorWin;
windowPref -topLeftCorner 137 719 -widthHeight 315 730 -parentMain true createRenderNodeWindow;
windowPref -topLeftCorner 341 426 -widthHeight 450 510 -parentMain true newProjectWindow;
windowPref -topLeftCorner 197 286 -widthHeight 774 767 -parentMain true scriptEditorPanel1Window;
windowPref -topLeftCorner 312 335 -widthHeight 414 183 -parentMain true myWindow;
windowPref -topLeftCorner 341 426 -widthHeight 388 93 -parentMain true theWindow;
windowPref -topLeftCorner 370 602 -widthHeight 258 64 -parentMain true myControlWin;
windowPref -topLeftCorner 183 327 -widthHeight 647 667 -parentMain true FBXEXPORTWINDOW;
windowPref -topLeftCorner 273 -33 -widthHeight 962 500 -parentMain true FbxWarningWindow;
windowPref -topLeftCorner 341 426 -widthHeight 384 411 -parentMain true pluginManagerWindow;
windowPref -topLeftCorner 61 66 -widthHeight 661 570 -parentMain true visorPanel1Window;
windowPref -topLeftCorner 246 1372 -widthHeight 428 500 -parentMain true toolProperties;
windowPref -topLeftCorner 467 478 -widthHeight 500 300 -parentMain true UVSnapshotWindow;
windowPref -topLeftCorner 341 426 -widthHeight 252 92 -parentMain true NormSzwnd;
windowPref -topLeftCorner 308 390 -widthHeight 387 437 -parentMain true mainWindow_OVERBURN_PPLE;
windowPref -topLeftCorner 341 426 -widthHeight 340 280 -parentMain true PluginInfoWin;
windowPref -topLeftCorner 124 821 -widthHeight 396 818 -parentMain true blastwindow;
windowPref -topLeftCorner 341 426 -widthHeight 402 217 -parentMain true polySoftEdgeWnd;
windowPref -topLeftCorner 118 1389 -widthHeight 789 488 -parentMain true hyperGraphPanel2Window;


These are my settings or for the more lazy I have attached a copy