Power loss with Specialized Tranisition Cranks?

I bought a 2008 Specialized S-works earlier this year and only used it in a couple of races and have trouble getting dialed in properly. Now that I have it dialed in, I have tried to do CompuTrainer interval and TT workouts with it that I was normally doing on my Specialized Tarmac SL. The problem I found was that it was much more difficult on the Transition. The seat heights are roughly the same but the seat-to-BB distance is obviously smaller for the TT bike (approximately 1in vs. 4in) but I can move back in the seat to similar a road bike position. I understand that you’ll obviously lose some power when in an aggressive aero position but I’m seeing this while riding on the handle bars on the TT bike. I see about 40W or more difference! My Transistion BB/crank has been making some grinding sounds out on the road (although less than 12 total rides after purchase though) so I just had it maintenanced and lubed up. Hopefully this does the trick. If not, has anyone else seen this or a similar problem? I’m temped to throw my old Aegis TT bike on the CT to see how the wattage proflies differ between the road and the 2 TT bikes…