Seems EMALS has another problem: too much stress on the airframe of the launchee.
Which pretty much has to mean: the acceleration profile is too sharp.
Is this not programmable? Were I designing such a beast, the timing of the electroflanger would be controlled by some manner of programmable devices, with parameters set at launch time, and there'd be selectable profiles for various scenarios. So correcting for "Oh, dear, we're yanking the nose wheels off the planes" would involve changing a few numbers.
Also, shouldn't the starting point be to match the profile of the existing steam catapults?
I know some aspects of the control system are archaic, but is the timing really hard-wired?
Afterthought: ... Or is the problem that the poles of the linear motor are far enough apart, and the drive binary enough, that there's excessive vibration? If so, shouldn't someone have noticed the issue early in development? Did Engineering notice it, and Management proclaim that the project must proceed regardless?