Homing the Z does not mean that it's automatically perfect. You need to level the bed to make sure. Leveling procedure is to bring the bed to the glass and trying to slip a piece of paper underneath the hot end. You'll want to do this at 3 points on the bed, right about where the leveling screwhead are. If it doesn't go through at all, then your bed isn't level and will cause the symptoms you are seeing. You'll want to do this with the extruder and bed on so that you take into account the heat expansion/contraction when printing.
If it slips under too easily, you're too high and you have to adjust the leveling screws for the bed. Counterclockwise drops the bed and clockwise raises the bed. These fine tuning adjustments should be checked before every print, but I usually do it about every time I turn the machine on and before I run a print. It doesn't take long. if you're using glass, you've probably printed the underbed screw caps so that tuning it can be done easier without having to remove the glass and punching through the Kapton on the bed.
EDIT: Remember, the z-axis screw that hits the endstop is for gross aligning the head to the bed, the leveling screws fine tune this to make sure that you're close enough to extrude but far enough that you can lay down plastic on the bed.