It'll be the wheels. I test rode a current CR1 albeit the Top o range Dura Ace one with Dura Ace CL24 wheels, it flew! I do a lot of racing and have ridden my share of top end carbon road race bikes and this was as fast as most.
The CR1 does however damp the road fairly effectively making it seem slower, but not actually against the watch. The Scott Rep in the North actually has a CR1 as his personal bike despite having the pick of the range, he's a Time Trialist by choice so wouldn't use a slow bike!
Get your position sorted so it's comfy. People seem to think that road race bikes have to be low as a worms belly and stretched to hell, the best position is one that doesn't cripple you but allows you to get good power out, comfy isn't always sat bolt upright either, my back kills if I raise the stem too far!
Then try some new wheels if budget allows, no need to go crazy. open pro on some reasonable hubs with a good build will be much better than loads spent on factory built fancy pants wheels. Do save budget for good tyres and tubes though. I use Schwalbe Ultremo ZX personally, 25's if you can find them as the roll better and are faster than 23's, not that expensive if you shop around, fast tyres that grip well.