One possibility is that you have figured your zones wrong. Certainly wouldn't be the first time it's happened.
I do find myself using slightly different gearing than many people might, in real riding and spinervals. Usually, I just go for what mimics my actual riding style, unless I'm trying to improve a specific weakness. I'm a spinner myself (105-110 rpm), so I usually use a smaller gear. If the workout is for stomping up short climbs or a TT-type effort, a bigger gear may be in order. It really depends on what your goals for the workout are.