Differences: weight; gearing; geometry; stiffness. I would think that each of these could affect the ability to get the power down.
Spit-balling here ... Perhaps eliminating one or more of those aspects could help narrow down things:
- Geometry -- any differences in your effective top tube length, reach, height of seat off the BB? If significantly different, I'd think it could impact your efficiency.
- Gearing -- how about testing the same ride routes with the same gearing?
- Weight -- load up on the lighter bike, to equalize your overall weight, so weight differences aren't the issue.
- Stiffness -- investigate the tubing, any deficiencies such as cracks or stress weaknesses in areas such as the BB that could impact how the power is delivered.
- Tires -- does one have a stiffer, stronger center bead for clearly reduced rolling resistance, versus the other type, despite being similar in size and pressures?
- Possible binding in the wheels/gearing -- remote possibility, probably.
- Placebo effect -- you knowing you're on the "offending" bike, hence feeling like it's more of a chore than it really is?