Ahh, all is clearer now.
If I right click the glossary list to create a new glossary, which is what I have been doing, the prompt for the type of glossary does not come up, it goes straight to my InstantTextWNP>Glossary folder with only the option to change the name of the .xlgo file being saved.
The prompt only comes up when I use the View current glossary - Glossary Viewer>File>New - I had not been using that option which is why I was not seeing the prompt and why I was confused.
Thank you Emmanuel