I'd say measure again... you're missing something. Be sure to look for any radius at the root of the shaft that could possibly be interefering with the elements that are sliding onto it. Otherwise, something is NOT the same between old & new. Put the old back on there if you run out of things to check & just need to prove to yourself where you are. Also, try the old nut just for grins... that's the easiest thing to check after it has all been reassembled. BTW, you didn't put a washer/spacer in the wrong sequence somewhere, did you??? I don't recall the exact component configuration there, and don't want to look it up right now, but thought I'd throw that 'generic' concern out there.
Lastly, what kind of measuring tools are you using? Tolerance "stack-up" can combine quickly if a little is added here, and a little added there, so if you're trying to compare measurements, old-to-new, you need to be measuring precisely.
My best guess is that you're not seeing a full engagement of the shaft (root radius or ???), but w/o seeing things, it's hard to speculate.