tire size could make a difference, but not that huge.
I have two bikes that I ride regularly, if I match cadence with my friend on one bike I match him with speed, if I match up on the other bike I'll pass him in a few stroke, gears are the same, but tires on the 'faster' bike are 27x1-1/8, matching bikes both have 700-25's
39/27 will be 39/27 regardless of the crankset, 1.44:1 is 1.44:1, rim/tire size is the only thing that will change effective gearing if both bikes have the same gears.
If you hadn't counted them and just 'felt' that they weren't right, I'd blame it on the altitude.
Ken.