So the thermostat probe is at the bottom of the tub, heat panel at the top. The thermostat is set to 90 and the thermostat probe is reading 90, but your probed thermometer is reading a much lower temperature. Did I interpret everything correctly?

If so then I suspect that your probed thermometer is bad, or your thermostat probe needs to be replaced. A 40 watt panel is more than enough to heat a your tub. One of your temperature probes must be off.