Spindle speed should not affect the pitch, as when threading, the Z axis should be geared to match the spindle, so even if the actual spindle speed isn't as requested, the Z should adjust to create the required pitch/thread.

Are you 100% sure it's a 1024 PPR encoder you have?
If it was actually 1000PPR, it would throw your pitch off by about 1%, and going by the 1.475/1.5 it's off by 1.66%.
At that big a pitch with a normal nut, being 0.6% off on pitch would probably still work without any noticeable problems.

Have you checked your Z axis calibration over a larger distance?
Checking over only 1mm isn't likely to show any minor discrepancies. I'd check it over whatever the biggest distance you can using a set of digital verniers/calipers