Assuming the fins are Tuttle base, very carefully sand the front or rear edge bearing surface of the base until it is a perfect fit in the tighter box. Then in the larger box insert a thin plastic 'packer' strip at the front or back when fitting the fin.
I cut these from the lids if butter or margarine tubs and have a stack of them in my spares box. Make them a bit narrower than the box width and slightly shorter than the end of the box you are fitting them in so they sit on the bottom of the box but don't protrude out the top when fitted. Also, fit you fins in a sheltered areas when using these 'packers' as it's annoying when they blow away as you try to fit them!

I have seen people use Mylar strips and strips of Coke can aluminium as well.

Oh, one more important thing. I have found that some Tuttle boxes are made a tiny bit too shallow (or the fin bases are made too deep). Check that is not the problem before doing the above operation!