At least with Slic3r (not sure about other slicing programs) the gcode will have M190 and M102 code to set bed temp and hotend temp. So if you have 60c for the bed in EEPROM and M190=100c, it will adjust to 100c during the execution of the gcode. At least that's how it works for me. Be sure to set you temps in the slicer to match what you want to print at. Also, if you have custom G code being inserted by your slicer, this can also be different than what you think you are setting since this can be a different setting than what you set in you slicer to generate your gcode. If you notice heating at one temp then suddenly heating or cooling after it hits set temp, look at these items and make sure they match what you want to print at.