I'm just thinking out loud here...but maybe it'll help. What things affect speed?

1) overall weight of a bike
2) rotation mass of the bike
3) rolling resistance of tires
4) fit/position
5) aerodynamics
6) drivetrain drag
7) gearing
overall weight of a bike, assuming you aren't going from a 15 pounder to a dutch cargo bike, should have very little effect on "speed." Rotating weight plays a much larger role.

I am also having a hard time buying any measurable effect due to rolling resistance of tires, assuming tires are reasonably similar from bike to bike.

What is "drivetrain drag?"

Why would the gearing matter? If you are riding the same gear on both bikes, it doesn't matter what your lowest gear or highest gear is...unless you are letting the gears choose you instead of vice versa? Bikes don't have automatic transmissions--you choose the gears. The only time it would result in "slowing" is if you are spinning out your biggest gear...and I kinda doubt that is what is happening.

My hunch is that any measurable "slowing" has to do with whatever changes have occurred in your position, particularly all the variables involving your saddle position. That is where your power comes from. Any change in saddle height, saddle fore/aft, or seat tube angle can have an effect on your power and ability to turn over the gears.