Added SDL_SetWindowPosition() call to SDL_SetWindowShape(), going to see what this does on Windows.

src/video/SDL_shape.c

@@ -240,6 +240,7 @@ SDL_SetWindowShape(SDL_Window *window,SDL_Surface *shape,SDL_WindowShapeMode *sh
     result = window->display->device->shape_driver.SetWindowShape(window->shaper,shape,shapeMode);
     window->shaper->hasshape = SDL_TRUE;
     if((window->shaper->usershownflag & SDL_WINDOW_SHOWN) == SDL_WINDOW_SHOWN) {
+        SDL_SetWindowPosition(window,window->x,window->y);
         SDL_ShowWindow(window);
         window->shaper->usershownflag &= !SDL_WINDOW_SHOWN;
     }

src/video/win32/SDL_win32shape.c

@@ -105,11 +105,11 @@ Win32_SetWindowShape(SDL_WindowShaper *shaper,SDL_Surface *shape,SDL_WindowShape
     /*
      * Set the new region mask for the window 
      */
-	mask_region = CreatePolyPolygonRgn(polygons,polygonVertexNumbers,num_rects,WINDING);
+    mask_region = CreatePolyPolygonRgn(polygons,polygonVertexNumbers,num_rects,WINDING);
     SetWindowRgn(((SDL_WindowData *)(shaper->window->driverdata))->hwnd, mask_region, TRUE);
 
-	SDL_free(polygons);
-	SDL_free(polygonVertexNumbers);
+    SDL_free(polygons);
+    SDL_free(polygonVertexNumbers);
     
     return 0;
 }