Maybe the step-height is wrong on the flywheel. If it's off by .002" it's enough to make it drastically different on the pedal. But before suspecting that, I would check to make sure the slave cylinder isn't pre-loaded. If the clutch master cylinder is adjusted properly, it might not be letting all the pressure off the pressure plate, and your clutch won't fully release. Usually this won't be accompanied by grinding gears, but it can in rare cases.

Get that thing sorted out. I want to see you at Dyno Day.