I don't know what to say, besides that I finished my project by using my method and it worked like a charm. But I only did full body morphs. Haven't done individual body parts. And also remember that you have to export your figure as it is on your scene (with all rotations and translations, morph it like that, and export it back like that). If you morph one zeroed body part and try to apply to a non-zeroed figure (and vice-versa), I'd foresee that problem happening.

I'll check out this Silo software you mentioned. Despite my deepest love for 3D Studio, I don't think it's the best option for modeling.