Ok its sorted now.
On the old style controller the trigger pins top middle and bottom for the right trigger. Had the output of the timer going to the middle trigger pin and the negative from the timer going to the top pin......
Microsoft seem to have made changes to these pins.
On the new controller the negative is now on the bottom pin but when you connect your timers negative to this pin you get the problems i mentioned in my first post.
The solution is to solder your timers negative to a different point.
On the new model if you flip over the circuit board to the side that you can see all of the triggers and the battery springs ect, with the triggers at the top. Look to the right side of the left rumble motors connection you will see 4 big blobs of solder in a square pattern. I soldered my timers neg to the bottom left corner blob.
I put this on here incase anyone else has this problem, this solution worked for me, i dont know why the rapid fire affetected my movement and aiming when it was activated but by soldering the negative from my timer to a different point it was cured. Even though when testing with a multimeter the 2 negative points are on the same single circuit.
Does anyone know why this happened because i cant understand it.