The Gekko does not report the lowest temperature on the dive. It only logs one temperature: the temperature at the deepest depth. As the temperature readings are quite laggy (especially if you have the Gekko tight against a neoprene sleeve), you will likely see a significant difference between the logged temperature and the coldest temperature.
I need to verify this, but I believe the logged temperature is the temperature reading at the time in your dive at which you first reached your deepest depth, not the temperature reading at the time in your dive at which you were last at your deepest depth (with depth being quantized to the precision of the log). If it were the latter, it could be closer to the actual temperature at the deepest depth of the dive, as the temperature sensor would have had more time to approach equilibrium.