Are you setting your Z offset with the bed heated? I always set Z offset with the bed heated, and after running a G29 command, so that the offset accounts for the bed mapping stored by G29. Also, it is important to have the bed heated to printing temperature because of the expansion that occurs. I have noticed my bed is significantly higher (and hotter) under the "Mak" in makerfarm. I suspect this hot spot, along with imperfectly shaped glass and a bed that hasn't been leveled in 6 months (in my case), throws off the offset values before/after temperature, which isn't a problem after compensating with ABL.