fin height differences
I recall when it was time to mount the fin on the fuselage, there were two different measurements on the plans for the height to set the fin on the aft fuselage bulkhead before match-drilling. An old dimension had been replaced by a new one, then the new one crossed out and the old one written in again.
I vaguely recall that there was even a written dimension in the text of the instructions, but can't swear to that.
ANYWAY, I mounted the rudder on the fin, test fit the fin to the fuselage, and found that the revised fin height dimension caused this exact problem, whereas the original dimension worked right. So I did that.
My kit was before the full matched-hole -1 fuselage. The newer matched-hole kits are probably different here. But if your kit is the same vintage as mine, this is probably what happened to you.