Lennart Borgman wrote:

>I think this helped me to realize what is happening. I am not quite sure but
>I believe this is a good guess:
>
>*** This is where the tooltip window gets created (I did not check further
>to see if it where reused, but the timings suggests to me it is not):
>
>  
>
>>>>>w32fns.c >>>>
>>>>>          
>>>>>
>void
>my_create_tip_window (f)
>     struct frame *f;
>{
>...
>  tip_window = FRAME_W32_WINDOW (f)
>    = CreateWindow (EMACS_CLASS,
>...
>      FRAME_W32_WINDOW (SELECTED_FRAME ()), /* owner */
>...
>      NULL);
>...
>}
>
>
>*** There is a SELECTED_FRAME above. As far as I understands it
>SELECTED_FRAME is set by operations that Emacs recognize.
>  
>
It is probably a bug if focus gained messages from the OS do not set the 
selected frame, but no new Lisp hooks should be needed.

It does seem that any input prevents these focus problems, so it is 
possibly a case of a message being sent between the UI and Lisp threads, 
but not getting processed until input arrives.