Changed flags and positioning (for the fake-hiding) as Andreas recommended.

src/video/SDL_shape.c

@@ -32,11 +32,12 @@
 
 SDL_Window*
 SDL_CreateShapedWindow(const char *title,unsigned int x,unsigned int y,unsigned int w,unsigned int h,Uint32 flags) {
-    SDL_Window *result = SDL_CreateWindow(title,x,y,w,h,flags | SDL_WINDOW_BORDERLESS & !SDL_WINDOW_FULLSCREEN & !SDL_WINDOW_SHOWN);
+    SDL_Window *result = SDL_CreateWindow(title,x,y,w,h,flags | SDL_WINDOW_BORDERLESS & !SDL_WINDOW_FULLSCREEN & !SDL_WINDOW_RESIZABLE);
     if(result != NULL) {
         result->shaper = result->display->device->shape_driver.CreateShaper(result);
         if(result->shaper != NULL) {
-            result->shaper->usershownflag = flags & SDL_WINDOW_SHOWN;
+            result->shaper->userx = x;
+            result->shaper->usery = y;
             result->shaper->mode.mode = ShapeModeDefault;
             result->shaper->mode.parameters.binarizationCutoff = 1;
             result->shaper->hasshape = SDL_FALSE;
@@ -239,9 +240,10 @@ SDL_SetWindowShape(SDL_Window *window,SDL_Surface *shape,SDL_WindowShapeMode *sh
         window->shaper->mode = *shape_mode;
     result = window->display->device->shape_driver.SetWindowShape(window->shaper,shape,shape_mode);
     window->shaper->hasshape = SDL_TRUE;
-    if((window->shaper->usershownflag & SDL_WINDOW_SHOWN) == SDL_WINDOW_SHOWN) {
-        SDL_ShowWindow(window);
-        window->shaper->usershownflag &= !SDL_WINDOW_SHOWN;
+    if(window->shaper->userx == 0 && window->shaper->usery == 0) {
+        SDL_SetWindowPosition(window,window->shaper->userx,window->shaper->usery);
+        window->shaper->userx = 0;
+        window->shaper->usery = 0;
     }
     return result;
 }

src/video/SDL_sysvideo.h

@@ -141,8 +141,8 @@ struct SDL_WindowShaper
     /* The window associated with the shaper */
     SDL_Window *window;
     
-    /* The user's specified SDL_WINDOW_SHOWN flag, for use once the user gives the window a shape. */
-    Uint32 usershownflag;
+    /* The user's specified coordinates for the window, for once we give it a shape. */
+    Uint32 userx,usery;
     
     /* The parameters for shape calculation. */
     SDL_WindowShapeMode mode;

src/video/win32/SDL_win32shape.c

@@ -32,7 +32,7 @@ Win32_CreateShaper(SDL_Window * window) {
     result->window = window;
     result->mode.mode = ShapeModeDefault;
     result->mode.parameters.binarizationCutoff = 1;
-    result->usershownflag = 0;
+    result->userx = result->usery = 0;
     result->driverdata = (SDL_ShapeData*)SDL_malloc(sizeof(SDL_ShapeData));
     ((SDL_ShapeData*)result->driverdata)->mask_tree = NULL;
     //Put some driver-data here.
@@ -101,7 +101,9 @@ Win32_ResizeWindowShape(SDL_Window *window) {
     if(data->mask_tree != NULL)
         SDL_FreeShapeTree(&data->mask_tree);
     
-    window->shaper->usershownflag |= window->flags & SDL_WINDOW_SHOWN;
+    window->shaper->userx = window->x;
+    window->shaper->usery = window->y;
+    SDL_SetWindowPosition(window,-1000,-1000);
     
     return 0;
 }

src/video/x11/SDL_x11shape.c

@@ -40,7 +40,7 @@ X11_CreateShaper(SDL_Window* window) {
         result->window = window;
         result->mode.mode = ShapeModeDefault;
         result->mode.parameters.binarizationCutoff = 1;
-        result->usershownflag = 0;
+        result->userx = result->usery = 0;
         SDL_ShapeData* data = SDL_malloc(sizeof(SDL_ShapeData));
         result->driverdata = data;
         data->bitmapsize = 0;
@@ -75,7 +75,9 @@ X11_ResizeWindowShape(SDL_Window* window) {
     }
     memset(data->bitmap,0,data->bitmapsize);
     
-    window->shaper->usershownflag |= window->flags & SDL_WINDOW_SHOWN;
+    window->shaper->userx = window->x;
+    window->shaper->usery = window->y;
+    SDL_SetWindowPosition(window,-1000,-1000);
     
     return 0;
 }