ok got it working
through a bizarre series of events
I had 3 finger dragging enabled in gestures and the standard 2 finger page flip, default for safari.
I changed the 2 finger page flip to 2 or 3 fingers, then it worked in chrome, 2 and 3 fingers. But my 3 finger select/move window gesture wasn't working so i changed the page flip back to 2 fingers and the re-enabled 3 finger drag and chrome is still working with the correct 2 fingers.
Weird bug but at least its working (haven't rebooted yet).