I'm using SciTE 3.5.0 and if I'm going to the menu bar -> File -> "Save As..." and then opening another buffer with the terminal or the file manager (check.if.already.open is set to 1) it gets the focus and is also the one which gets then saved. Maybe it should be ensured that always the buffer that called the saving subwindow should get saved (for example if the saving subwindow is opened by not giving new buffers the focus and not overwriting unmodified untitled buffers).
You should see a warning message:
File "x" is already open in another buffer.
I'm not seeing this warning but I'm also not opening the same file.