Interesting. I have not heard the two different speakers, but according to the klipsch website changes were made to the drivers and crossovers. Maybe they made it sound worse, it is possible.
Also, it appears from the specs, that the old centers used 2.5 way designs and the II's do not. A 2.5 way design would be superior to a 2-way design especially for the center speaker to reduce comb filtering.
Some believe in break in and some do not. I think that some speakers and headphones definitely do benefit. Try breaking the rc-62 ii and compare again.
Do the 6.5" drivers on the rc-62 ii sound different to each other? If they sound different, then probably still 2.5 way design.