I have this problem as well. But with mine the under hair starts off curly or at least wavy and then as the day goes on or my 2nd day hair the underneath is straight. My hair is halfway down my back when it's straight so it is crazy noticeable.
I believe the under hair is just a lot more delicate and therefore didn't take too well to the years of straightening (though not often), coloring (which I haven't done in 2 years) and being chemically straightened (which I've done twice in my life).
My only fix for this is to get the straight parts cut shorter than the rest of my hair. I figure since it's only the underneath you wouldn't even notice they were straight if they didn't stick out under all the rest of the hair by 2-3 inches at times. Lol. So I've tried explaining this to my stylist 3 times, they haven't gotten it right yet, but I'll keep trying cause it makes sense to me.
started no-poo on March 15th, 2010
co-wash - Suave Coconut
rinse - (once a week) Bragg ACV
conditioner - GVP Conditioning Balm
leave in - Kinky Curly Knot Today w/ Honey
microfiber towel, wide tooth comb (sometimes) and air dry!
all that = HAPPY CURLS!