The weight of our bike and you should compress the suspension a little at rest. Optimally with you sitting on the bike the forks should be compressed 1-2 inches, putting you somewhere in the upper middle of the suspension range. The forks have to deal with bumps AND dips in the surface to keep your front wheel planted firmly on the tarmac. If the suspension front or rear tops or bottoms out regularly in normal riding something isn't right.
What rate springs did you get?
What weight fork oil did you use and what amount of oil?
Did you use the old short spring as well as the new spring, or the spacer tube, or just the Progressive Suspension spring?
How far out of the inner leg did the springs stick out before you put on the top cap? Optimally there should be around 1" of preload compression (spring length at full extension minus compressed (installed) length in a nutshell)
I did the Progressive Suspension springs and the Race Tech valve emulators on my bike a few months ago. Straddling the bike I can rock it, compressing the rear and get about 1" of extension from the forks, maybe a little more when I throw the bike up in the lift (1 1/2"). I had about 1 1/8" of preload compression when I installed the top caps. I run roughly 13 weight Bel Ray fork oil (60% 15w 40 % 10w) and originally set the fluid level 5 inches from the top of the extended fork with the springs out, and I have since added maybe 1/2" of oil.
The people at Progressive Suspension are knowledgeable and helpful with set up info, as were the people at Z1 where I got my Progressive Suspension shocks and fork springs from.