First of all, it is very important to verify that the illumination conditions during the capture of the reflectance targets are representative of the illumination during the flight. Make sure that there are no shadows on the reflectance target nor on the sunshine sensor, and neither reflections onto the reflectance target from adjacent objects or yourself, and that the general illumination didn’t change (for example due to clouds forming). Make sure to hold the camera horizontal, and align the target horizontally and facing North.
Secondly, if you are using PIX4Dmapper, remember that as mentioned in the knowledge base, the sun angle correction assumes clear sky. If you have overcast conditions, please select “Camera and Sun Irradiance”. In PIX4Dmapper, selecting sun angle corrections in cloudy conditions leads to biases. In PIX4Dfields, you select the weather conditions in the settings.
For further investigations, I would suggest to plot the reflectance target derived sensitivity as a function of the weather condition. For those cases where the sensitivity is quite different across bands for the same flight, I would suggest to check if you selected images from the same capture for the different bands. If you mix two different captures that were acquired in different illumination conditions, you get biases. In general, I would suggest to always note down the weather conditions during a flight and take a few pictures of the sky with your mobile phone to visualise the in-situ conditions to refer to them later.