True, the SDP40F was basically a passenger version of the SD40-2, but as several have said, there were frame and truck differences. The BN didn't have any serious problems with them, and they performed fine on the Empire Builder. I doubt that the weight of the fuel/water was an issue, as the BN bought other diesels with similar size tanks to avoid refueling stops. And, as Vince noted, many of the loudest complaints came from roads with poor track. It's possible they were simply too big, in length or weight, for the track conditions.
One magazine reported that an apparently unique problem on the SP was out of gauge wheels. This was finally traced to one crossing being out of gauge, and when the units hit it "at speed", the frogs were forcing the wheels out of gauge. Fix the crossing, and the units ran a lot better, and with less wheel wear. Whether the story was true I have no idea, but since wheels aren't held in place by anything except friction, I guess it could happen.