You say the wheels are not rubbing on the brake, but are the hubs spinning freely? It is quite common for hub cones to be overtightenend from the factory, perhaps hub bearings are binding a little? How many revolutions do you get for comparative-force spin on Trek vs BMC wheels?

When you compared the acceleration of Trek vs BMC, were you in comparable gears? Trying to accelerate from standing using too large/hard of a gear would be quite slow. Like if you tried to start a drag race in a car with the stick in 4th gear, doesn't matter how fast the car is, it's not gonna be quick off the line.