So, where was this store? Ann Arbor Michigan perhaps?
It would surprise me if they did in fact plan not to stock Unfit for Command, the bottom line is money. If they think they can sell the book they will. I live less than an hour from Ann Arbor and we have several Border's Bookstores in the area and have been told they have the book. I think it is just selling faster than stores can get the copies.
The Borders bookstore I visited was in a violently Democratic state - California but in a Republican subdivision - San Diego.