I have an object flying over a layer of spectral clouds. Everything looks good except I can't figure out how to get a shadow of the object to be render on the clouds. Is this not possible? 

Where is your light source?  Often in Spectral Atmo's the Sun is below the spectral layer and close to the Camera. 

Make sure you have cast/receive shadows turned on in the cloud texture.

Keenart may have your answer. Check the sun position, and check your objet's position. You may have shadows if you use more ambient light in your scene, but it may then be too bright.

The sun is slightly above the object and I am getting shadows on the cloud layer from the clouds and the sun. But nothing from the object. I'm not sure what is meant about turning on the receive shadows on the cloud texture as these are spectral clouds - I didn't set the texture I don't think......

You can still edit the material by clicking on it in the cloud layer, but if you are seeing other shadows, it's probably just an angle thing.  Put a big cube in the picture and see if you see shadows from it, as a test.

I have tried everything and changing all of the settings but cannot reproduce the missing shadow. If the Sun, object, and camera are not in alignment the shadow can wonder off the view as indicated by eldritch48.

Try using a spot light above object and in line with the Sun and see if it will cast a shadow onto the clouds. Pump the spot light up to about 1600 to 2000 and change to the color of Red, which should give you a halo around where the shadow should be and see if it is in the view.