Hmmm.. that's funny, I never get step fractures when I transition from direct to indirect.
Seriously, an irritating step fracture right from the get-go means two things depending on the thickness of your workpiece.
If you're really good at thinning the workpiece with direct percussion (bopper) and then transition to not-so-good indirect, it's normal to encounter problems . If you're really good at both, then you may be asking too much of the stone. It's VERY difficult to thin down a thin piece. The most important thing is to check the surface of the workpiece. Check it VERY carefully. If the surface is not convex, all the way from the platform to the intended end of the flake, then you will get a step. Flat/concave spots are very common and very difficult to knap through on thin pieces. They may also be very difficult to see. Try knapping with a light in front of you so you can angle the workpiece to see the shadows of the flake scars easily.
If the workpiece is still relatively thick, then beef up the platforms and knock off a couple shorter flakes to see if the step problem disappears. If you still get steps with a stronger platform and shorter flakes, then you need a LOT more force in your strikes. This is especially true with raw stone. A lot of guys are surprised when I show them just how much force I use when working tough rock. I smack it like I want to break it.