It's interesting how some things seem to "click" right away, while others don't, even if they seem similar on the surface. There are new actions I practice in rapier that slide right into place in my head, and others that seem like they should but don't. This becomes even more pronounced when I switch to an even slightly different sword form. It was the same way when I used to aikido, too.

Some of it is the newness, and some I think comes from your body thinking it knows what to do, but your mind saying, "Uh, no, actually, we need to do this instead..." Not just muscle memory, but also muscle assumption, if you will. Once you learn the bridge from the assumption to the form, the learning curve lessens (at least in my personal experience, YMMV).

The brain-to-muscle ratio is different for everyone. However, I think the fact that you are thinking the kicks through now, rather than later (when you need to "fix" an improper action), will result in tighter form overall.