Two different chains, same chain length, different wheelbase!

It's down to the size of the parts that directly sit on the freewheel and chainring.
If one chain has a slightly smaller diameter of "rollers" the the larger one will pull the wheel in slightly... I gather you are talking about a small amount of difference here?

Fixed

^swat I said. Pixies, interferring with your rollers.

(would'nt the old chain appear to be longer as the rollers would be worn?)