I was experiencing the same issue. Using just the link my company gave me I would only get the 7% discount. What I needed to do was go through the EPP link so i'm "logged in" as my company and then back out to the products pages where you can choose to customize a Mini 9. Then it picked up the $50 discount and the 7% discount when I went to check out.
Here in a sec I will see if I can double-check those steps, I gotta dig up my EPP link.
EDIT: I can not seem to get the website to apply both discounts at the same time. It may have either been a loophole for the last sale or i'm still missing a method, but I can't do it anymore.