Check the X axis for level, not the bed. If the X axis is not level and you adjust the bed to suit it then you're effectively printing a parallelogram! Both things could be parallel, but not perpendicular to the Z axis.
I set mine up by powering up the Z steppers (lift Z by 1mm) and then measure the distance from the X axis to the frame with digital calipers. I'll adjust the right hand Z axis by hand until the measurement is the same, and only then will I do bed levelling. That way I know its parallel and perpendicular.
Z drop is a well known characteristic of the CR-10S, and indeed the CR-10 when modified to dual Z. There are dozens of designs on Thingiverse to mitigate it, mostly toothed belts to keep the two motors in sync. I think a simple block to level the Z carriages before printing is probably simpler though
