Adjusting the saved as file format via the Alignment window Save As... dialog box doesn't actually change the format used to save the alignment

Saving an alignment as a new file will (rightly) prompt you to select a file format if you haven't.

Subsequently selecting a format and clicking 'ok' again says you need to select a file format.

Retrying the operation works successfully. I've managed to get Stuart to replicate this one, and have screen-grabbed the process (attached)