Well, clearly if the shape is so radically different, it must be texture space.... Far less likely to be some sort of bug.
I'm not even sure what you're talking about. Masked, or Final Position Final Density, or not, the clouds are the same, with "Move textures with clouds"...
The only difference is the cloud lighting model and edge softness. Perhaps you need to poke around your setup some more. Is your masking in final position or something that would not be effected by cloud layer settings?