The BB may be more to the front or the back of the saddle depending on the seat tube angle. This changes the way you hit the saddle as your legs are at a slightly different angle. This rotates your pelvis forward or back a little and you sit differently. Also if you have different length cranks this changes things too. Even if the BB to seat height is the same you bend differently with different length cranks.
I agonized over this for ages, you may need the saddle in a different place to be comfortable.
Try getting five identical saddles on different dimension bikes to feel the same... AAAAAH...
