I got the same issue while flying small test rocket with a TWR of at least 2.5 (I have only RA, not FAR).
The problem is that the drag increase a lot during the transonic phase of the flight (around 0.95 Ma, according to the KSP's AeroGUI); this, combined with the weight of the craft, can result in an opposite force higher than thrust, slowing down the rocket a little until the drag decrease after passing the sonic speed. The higher are the TWR, the lower this phenomenon is.
I think that this problem is related to the drag model of KSP (and not to RA), while FAR is using a better one.
PS: keep in mind that the TWR doesn't take count of the drag forces applied to the rocket during flight in atmosphere.