hey, i am sorry you had such a bad experience with borders. there's 2 things i would suggest you do.
1) either call or go back to the store and get the "customer care" number. it is a 1-800 number for customers to use to either complain or praise, mostly complain. they generally find a way to rectify the situation, and often issue gift certificates.
2) find your documentation. return all the books to borders. then repurchase them and present your documentation so you can get your discount.
i know it sucks when people are suspicious of you. sometimes i would just give the person the discount on homeschool stuff, or teacher stuff, and sometimes i would ask for identification. it depended on my mood, whether the manager was standing beside me, or whether the customer had been a pain in the ass.
some employees are suspicious of all customers because they have seen too many people working a scam. i've even had teachers try to use their discount on erotica!!! anyways, it is a sad fact of life that your shopping experience will vary widely depending on who is working when you shop. some employees are bitter, some are happy, and woe to you if you happen to get the bitter ones.
good luck rectifying the situation!