Hi los and faerieweb,
Sorry for the issues you are still having. Can you please both post in your own threads so we can give you our full support. I am afraid if we keep having multiple people post on the same thread we are going to miss something from you and I would prefer that not happen.
For faerieweb I looked at your site and it is a css issue hiding the minus quantity.
It is coming from this stylesheet in your theme:
themes/elision/css/woocommerce.min.css
Removing or fixing the styles in their should fix the issue.
For los not sure what is happening there, after you have done testing and if you still have an issue, please post in a new thread referencing this one what you find out.
Thanks