Pretty big bump, but just in case someone reads this... turns out its an issue specifically with the takeoff to ISS scenario for some odd reason. All the other KSC missions for it are fine.
EDIT: it actuallly doesnt appear to be solely mission specific. The ascent to ISS is broken 100% of the time, and some of the custom skin ones work most of the time, but not always. Not sure what to make of it
sigh found the problem... the joystick axis in Fly By Wire used for RCS apparently needed a deadzone, net effect was there was always a tiny RCS force causing an acceleration at all times. Discovered it by emptying fuel tanks to see if that had any effect, and emptying RCS did. To confirm, i tested with no joystick/fly by wire and it works fine.