Some modern carbon forks have the crown race molded as part of the steerer. The lower bearing is in direct contact with this molded race. If you put the old crown race on top of this molded race, the headset will not adjust properly.

Also, did you put the compression ring, or split ring, back in?

It sounds like you just need an extra spacer, due to steerer length diffrence, to be able to compress the bearings properly.