To clarify, you have an early "stubbed" 6MT and are using the later "male" 5MT axles. You pulled out the stubs and switched the seals to the "stubless" seals and the axle is bottoming before it seals.
Are you sure it's seated all the way? An easy way to check is to pull off the circlip from the end of the axle and then see how far in it will slide. I'd be willing to bet that you're just not getting the axle all the way in.