A result of the "Multiple Alignment" is drawn in color. So, the result is written in "Rich Text" format.
Because NotePad does not support "Rich Text" format, please use "Word" or other software that support "Rich Text" format.
Anyway, if you still need to use NotePad for pasting the result, after dragging over aligned sequences in the "Multiple Alignment" window and press ctrl-c, then paste to NotePad. The result will be shown in Notepad in monochrome.