It sounds to me like your temperature sensor is in a bad place - above the window means it is located high, perhaps too near the ceiling, and above a cool window which creates a downdraft and, thus, pulls the heated air off the ceiling to the sensor.
My AquaHot is an AHE-100-02S model, likely an older model than yours, has one electric element, and I regularly have both the electric element on with the diesel burner on. In fact, they are both on right now. The diesel burner kicks on only if the electric element/s cannot keep up.