The long box PS1 titles at my local stores are usually at fair-to-lower prices. I've always assumed this has to do with some belief on the store owners' parts that these early titles weren't so great or maybe just haven't aged well. I'm not saying this is the case. Just hazarding a guess, really, as I'm not too familiar with these games myself.

On the other hand, crazy markups are still the order of the day for pretty much any PS1 RPG they get their mitts upon.