Ryan, I haven't been having problems with Borders.com, I went on just to check and see if I was having the same problems as you were describing, and there were no issues with my cart.
Maybe it has something to do with the "Refresh" button. Try using that button when you first get onto the site, check your cart, try it again. Then, put something in and check it.
You know, someone told me once that when this happens - either your computer is old and/or not very good, or it has something to do with the cookies. That you have to delete your browser's History or something.