Thanks for mentioning forks, Sadie Kate. I've come to the conclusion that my fork is likely part of the problem, too. I went with an Alpha Q on the Moots. Great fork, but it's arguably too stiff for me. I really like the way the bike descends and the fork tracks, but it's not the comfy ride I wanted from my ti bike. I'm not ready to throw in the towel on it yet though. It's just too costly for me to change without REALLY being sure that it's a factor. That, and there aren't a ton of other options unfortunately. Plus, I am finally making some headway with the set up.

To the OP, you might also approach the problem from a different angle. Instead of figuring out why the Surly is less comfy, you might consider ways to make the Cannondale a little less harsh. What bar tape do you have on it? What tires are you running and at what PSI?