Maybe also a power supply issue... if the power supply is a bit weak, all the power goes to the heater and none to the processor, which then stops, which turns off the heater, and the processor then starts up again.
A heater cartridge is about 40W, say 3.5A @12V. Fans and processor and stuff need another amp or so. So you need a power supply that's good for a minimum of 5A, preferably a bit more.
An intermittent short between 12V & ground could also cause the system to reset.
May also be wiring faults; if the heater is on and the thermistor doesn't see an increase in temperature, the printer shuts down for safety. If there's a loose connection, it might not disconnect for some time. This could apply to either the thermistor or the heater. A short across the thermistor would have the same effect. When it is cooling down, is it showing valid temperatures? Does this happen when the print head is kept still, or only if it is moved around?
Toggle the Log Viewer on in Repetier Host and see if there are any error messages there.