Sorry to double post, but this just hit me. Over time, the footers will move so that could've just happened and that would affect the torque on a track and even alter the shape. That would definitely create some roughness.
/\ this isn't about older B&Ms, its about newwer ones. Hydra was the only coaster that actually hurt my ears riding. It was still fun, just very bumpy from what Im used to with B&M. I found it actaully smoother in the back half of the train then the front every time I rode.
After watching the Supercoasters show, I began to lean more towards the possibility that the fabrication of the track pieces could definitely have something to do with it.
They mention that even the slightest deviations in track fabrication can cause unecessary roughness on the end product. Maybe the tedious work involved in making this steel is taking a toll on the workers and theyre getting sloppy?