I know this is a really old thread, but I'm wondering if you ever got to the bottom of the cause?
I've got exactly the same issue with my 2nd to 3rd shift. Under very light throttle it kind of delays shifting, then bangs into 3rd. Worst in car parks, or when pulling away in traffic when the car in front goes slowly, so I have to lift off while pulling away gently. Even with just moderate load it's super-smooth. 3rd to 4th is always smooth.