heh.. what software are you talking about?
I'm guessing Maya, and I see the same issue. I don't have a solution to MMB, but the easiest answer is that the slight jump doesn't occur with LMB.
What annoys me more is that years ago, MMB used to manipulate things freely and it would not activate individual axes. This was great for quickly moving things in screen space without even having to look at your cursor. Now you have to avoid the gizmo to get this behavior, which usually means moving your mouse away from where you are currently working.