For reasons I won't go into here, I just had the frame replaced on my Stratus XP, with a new 2008 model. I also took the crankset from Charlie's (now Terrie's) SXP and had it put onto the new frame, since it had ~4,000 miles on it instead of the 14K mine did. I know they've changed the rear dropout and tubing angles slightly (where the rear wheel hooks in), but beyond that, the frame is the same for all intents and purposes.
When I got the "new" bike back, I immediately noticed that to get the same "feel" of seating/riding position, I have the seatback a full two notches further reclined. The other thing I noticed was yesterday -- I am getting a LOT of chain grease on the inside of my right calf from the chain hitting me when I'm in the 52T with the higher rear gears, whereas this was a very minor issue in the past with the old frame. I wiped it off at two different rest stops yesterday, and still had a bunch more on myself at the finish of the ride. It's like the chain is coming into the chainring slightly higher, and/or slighly further out to the right.
I'm not sure what's so different at the moment about the chainline vs. my seating position, but I'm going to do some careful comparisons to the two frames when I get home tonight.