Following up and what Yorkie has posted it is all down to maintenance.
The age of the rail/sleepers/ballast is of no major concern as long as the track ballast and fromation is in good condition, uncontaminated and drained.
Rough rides are the result of the response of the rail vehicle to the track geometry in the majority of cases.
It sounds as if the transition from CWR to branch line is poor, although there will always be a slight respoinse as the vehicle moves from CWR to jointed track. Lighter weight vehicles, particularly EMUs/DMUs tend to "feel" jointed track more because of that.
Poor track geometry on jointed track may manifest itself as either a "rolling" type motion or a "bouncing" type motion, and the poorer the track the more likelihood of both.
There will always be a more liberal response when travelling over jointed track, which is not always indicative of a problem, simply a reflection of the nature of the track type. I think in many ways it is because of the amount of CWR we now have on passenger lines, and the naturally much better level of ride this gives.
I hope this has answered the question.