MatterControl only has EEPROM mapping for printers running Marlin or Repetier firmware. Your printer is probably running a firmware which MatterControl does not recognize. You can still change the settings you need to, but you will have to do it by hand through the G-Code terminal. See the RepRap wiki on using the M503 and M500 commands.
Since it went away by itself, I would check, if sensor wires (end stop switches, temp sensor wires)and the hot end wires overlap. Maybe the current in the hot end wires causes some kind of interference with sensor signals.