I lowered the clutch by turning the bolt on the clutch assembly. Everything was fine for couple of days, enjoying the new feel and all. But then one morning it was noticeably harder to shift into gear. Once I got going it became smoother shifting. So I adjusted the bolt to about 2.5 turns rather than 3 turns before.
And everything was fine for about a month. The other day it was harder to shift than the first time I encountered the problem. I'm going to try to set the pedal back to stock position today.

Anyone know why I have this problem?

Well you most likely screwed up somewhere. Ive had it for about 6 months with no problems.

Maybe you're not tightening the nut enough so it's adjusting as you're driving? I've had mine adjusted for about 6 months now also, and no issues. I only went about 2 turns, but that was good enough.

Put it back to stock and put in the D-Wolf clutch kit.