The problem i was having was that unless i set a quantity for every variant the product would be out of stock, and when i set quantities on one option it seemed to delete the other options, even reinstalling SBA 1.5.2 didn't work

However when I updated to the latest version of the mod SBA 1.5.3,
(excellent and much improved readme by the way),
everything appears to work exactly as it should, I don't need to set quantities on options that don't need them