It sounds like you need to experiment with the white reference setting. As M42 is not an 'average spiral galaxy', this default setting may not be optimal for that object. The issue is - with about 50 choices, which star reference will give the best results? Maybe try researching some of the larger stars in image and use the setting associated with those...? As you know, it early days with this process, which means a lot of trial and error....
Also - are you using a background reference preview? This may help a lot.
Mike