Are they conventional or inverted forks on the bike?
I recently used the wrong measuring method on my brothers '98 900RR and found I was ending up not only pre-load internally, but pre-load again when I would go to screw the cap onto the end of the fork. I knew this wasn't correct so I took everything back apart and re-measured everything to find my numbers were correct by using the method I was measuring it with, but that was the problem, I was measuring it as though they were inverted forks and they were conventional!

Being that I had mainly done inverted forks in the past it was an easy mistake for me to make.
Conventional forks have the smaller diameter fork tube clamped in the triple clamp, inverted forks have the smaller diameter fork tube at the bottom of the fork (where the wheel is mounted) and the larger diameter is clamped in the triple clamps. The reason for this is by clamping on the larger diameter tube in the triple clamp it provides a more rigid assembly which is the reason you see this type of fork assembly on most performance sportbikes currently being produced (600 and above). Both my GSXR 750's have inverted forks but my '99 GSXR 600 has conventional forks, that's why I wonder if it's the same situation with your bike. Every bike I have done required the spacers being cut when using a RaceTech kit - but that's only been my experience so far so it's not a guarenteed thing.
