Hi Nickie,
For your Variants, which "Price Type" do you have selected?
On your Discount Setup page, do you have the "Enable Product Quantity Discounts" option selected?
Please also upload a screenshot of your Product Setup screen so I can view your base product's setup.
I just tried to replicate this issue in our test store but the quantity discounts seems to be applying all the way through checkout. You can view this Product at the following link:
http://www26.smith-consulting.com/Buy...
I would like to have you login to one of our public test portals and configure the cart the way you have your's configured and try to replicate the issue. This will determine if the issue you are reporting is with the latest version of the cart or an issue with your specific DNN portal/cart install.
Please a helpdesk ticket with a link to this post at the following link and I will provide you with credentials to login:
http://www.smith-consulting.com/Suppo...
Thanks!