Xtend is designed to remove black bars by expanding content to fill the empty space. If you don't have any viewports, Xtend will create one, so be aware that at least one viewport does exist.
It definitely doesn't enforce the original window size, though... that would defeat the whole purpose. Is your project configured to allow resizing the window? (This setting must be applied in GameMaker itself, not Xtend.)
If you're unable to identify the problem, feel free to send me your project by email (contact@xgasoft.com) so I can investigate and better advise.