Maybe double check your chain measurement with a ruler just to be certain, though they should agree.
2000 miles is significant, in suboptimal conditions (dirty/wet/lack of mantenance) that's easily enough to cause substantial wear.
Dura Ace 9000 cassettes have all cogs larger than 16t made from titanium, and titanium cogs are known to wear faster. I wonder if it's possible that a titanium cog could have worn faster than a steel chain?