Yeah, you're right. I find very convenient the procedure going thru to Milkshape to export animations to Cal3D and guess I'll stick to it, leaving Misfit as a second choice when things go wrong in the first place.
Though there's one thing I'd like to make some further research on: when I was working on a revisited version of my SCBA set, I rigged a section of the respiration tube bound to more than one bone (neck's and one of the spine, I think), so when the puppet wearing it turned his head, the tube would deform in a realistic way, more or less. Everything seemed ok both in FragMotion and Milkshape: the involved vertices were rigged to two bones, and with the weights totalling 1.00. But to my disappointment, everytime I've tried, every vertex was only influenced by just one bone (that of the greater weight) or none at all (if the weights were the same, ie 0.50).
So I'll now repeat the tests by using Misfit to generate the .caf files. I'll keep you updated on any progress.