I'm sorry for my english

I'm having a problem with the clutch inner basket.
I've bought a 2003 CRF 450R and I changed the old crankshaft with a new one. I also changed crank bearings, cam chain, head valves, cam chain tensioner, piston and rings.
Everything is OK, but I'm having a problem with the clutch inner basket (I had the same problem some months ago on a 96 CR125).
When I try to screw the nut to block the inner basket against the outer basket, the inner basket get blocked and if I try to turn it, it moves together with the outer basket.
This happens because when I mount the inner basket on the countershaft, the thread on the shaft (where I have to screw the nut) does not totally come out from the inner basket.
At the beginning, I thought because I added an extra washer between the countershaft and the bearing before to close the inner cases (and for this reason, the shaft could not comes out correctly) so I opened again the engine to check this condition but everything was OK, no washer was present, and so the countershaft can't come out more than it does now.
To solve the problem, I had the remove the 23x48 mm washer which should be inserted between the outer and inner clutch case.
Without this washer, the shaft thread come correctly out the inner case and so I can correctly screw the nut.
Can someone explain me why this happens, please?
Everything is mounted as stated in the manual, countershaft is correctly installed and also the outer basket is correctly installed.
Please, help me because I 'd like to solve the problem and I want to mount again the 23x48 washer as honda planned.
Thank you!