Good evening Geoff,
First off, I am sorry for the late reply.
As you might have read, our team was unfortunately away on the annual team retreat.
I apologize for the delay this has caused.
You are right about the only remaining issue: the quantity bug is not related to the theme.
This means that the conflict lies elsewhere.
Based on what I am seeing on your install, it looks like WooCommerce needs to run an update of the database to work properly (there is a notice for that).
After a database backup, I would recommend running that update and seeing if that helps.
If it does not, our only other option would be to temporarily deactivate all other plugins (even other WooCommerce extensions) until we find the culprit.
Let me know how that goes.
Best regards,
Geoff B.