I can only speak to my experiences.
There are TONS of places to loose power, but generally position and wheels are the most important thing.
I never really found one particular frame 'flexy' enough to loose power over another, BUT I'm small and pretty light, so if you're big, the frame itself could have a major impact on your speed.
As others said before, how well do your wheels spin? what tires are you using?
both of these can have a Major impact on your overall speed.
Most of my experience is with an Aluminum Corsa. You can purchase a used one on a regular basis for about $1500. I've seen them under $1k occasionally.
I don't have any official results to point to, but if you take my work for it, I was able to place 13th out of nearly 70 in a 2 mile USAC sanctioned (cat 1,2,3,4 and 5) hill climb on my Corsa (weighing 25.6lbs) earlier this year. I also competed in a 10 mile TT last weekend where I finished with an average speed of 27.4 mph.
My point is, there is nothing wrong with the Corsa at all. In fact all of the Bacchetta line is pretty similar to the Corsa in terms of build quality and configuration. It's possible to configure all of their dual big wheel stick bikes nearly the same and have similar performance.
You mileage will vary on your fitness level, seat recline, handle bar type, and wheels.
I can't speak to other bikes, but I can stand by the Corsa having put about 20k miles on it over the last few years. There is a massive amount of performance that can be wrung out of one.
T