Do they both have the same tire on them? If not switch the tires and see what happens.

Geo plays a part, any weight difference in the wheelsets might (rotating weight is what you feel more than overall bike weight), a difference in your position (if you aren't at optimal efficiency and are closer on one bike than the other you may be noticing a power difference), some would claim build type (some bikes are built "stiff" and take all that power to your back tire and some are built softer which can be more comfortable but may loose you power from pedals to wheel in flex).

Lots of science crap goes into that unfortunately. Pinning down exactly why would be difficult.