I had RMAed my original FTW 1080 as well and received the new card November 7 with thermal pads installed. Like your situation, this new card clocks much higher than the original one I had. Below is a link to a Time Spy score at clock +125/memory +400. That's a graphic score of 8057 and an overall score of 7584. Sweet, and I've never had a score this high with the previous card.
I agree with what Sajin says about perhaps your clocks aren't stable as I have seen with some friends that additional boosts to clock OR memory can produce a lower score. In my case I know this FTW 1080 thermal mod card could take more than the clocks I used but frankly I'm not interested in trying. I only OC to see how the card runs with an OC in a benchmark and then it goes back to defaults for gaming.
http://www.3dmark.com/3dm/16048877 And here is my Firestrike score, 19247. Didn't hit the 19K mark with by original card.
http://www.3dmark.com/3dm/16048975? PS: with my original card I clocked at +110/+400 as the core wouldn't take much more than 110-114.
PPS: most important to me is the original card at stock never went below 1898 core in gaming. That wasn't bad but with the new thermal mod card and the same fan curve this new card doesn't go below 1924 while gaming. Double sweet.