Gearbox oil level 4.0 auto

Ok folks I am a tad confused I recently did a full service on the truck.
I dropped the gearbox oil and rather than just putting the recommended amount back in ( not the 9litres+ dry fill amount)
I topped it up using the dipstick and it was bang on the top mark this only equated to 4 litres being put back in.
On periodic checks of the oil level it has shown that there is now an excess of ATF in the tranny not a lot but enough to make me want to drop some out.
Has anybody else come across this issue ?
I check the box according to the manual, vehicle cold, start up, into 1 st then back to park then check the dipstick.
I have noticed the dipstick has stamped on it check while cold and in neutral which I have done and still get a higher level.
Any help greatly appreciated