Sac RT had a serious problem with some parts of the newer (concrete ties) track beyond Sunrise Blvd. In places, the corrugation was more like bumps that got into resonance with the CAF car (but not the Siemens - they rattled a bit but didn't bounce) suspension/wheels at just under 55 - vertical bouncing that was very bad. Eventually, they got a grinder out on that part of the line (and a few other iffy spots too) and the ride issue doesn't seem to occur any more - but now the CAF cars howl in the spots that were ground. So is it possible that we've exchanged higher/longer-wavelength corrugation for shorter-wavelength that induces howl?

There are well-developed physical theories for how corrugation in general (on roads, rails, whatever) forms. There was an extensive article many years ago in California Geology (now defunct) about how large corrugations form on off-road motorcycle hills (the examples being in a ORV area near Coalinga that's now closed because of the large amount of asbestos in the dust).