Is Thrifty Car Hire Selective Towards Foreigners?

I was turned down at the collection desk for having a foreign passport (though I have permanent residency in SA and have been here for for 14 years) whose number is different from my South African Driver's Licence number (which I've had for 9 years). My Passport Number and my SA Driver's Licence number will NEVER match, that's why my Driver's Licence number has my traffic registry number. I have used the same DL to buy cars here in SA, to drive here in SA and to hire cars from Thrifty's competitors such as Europe Car and Avis...without a problem since 2012 to date. Worse of all, Thrifty's online booking system even asks for and accepts passport numbers! Was so inconvenienced when I was turned down at the late hour and was forced to search out alternative means! Please pay back my partial deposit! its way overdue!