I've been researching this and see a lot of papers and appnotes that are mostly the same.
We conjecture that some capacitive-DAC pipeline ADCs do not act as if they have a single sample-and-hold in the front end, but are more complex and have, essentially, multiple s/h elements. One consequence is that the presence of very high frequency components of the signal can cause missing codes if the sample aperatures are not absolutely identical. I think we may be seeing this happen.
Sometimes we deliberately add dither noise to improve ADC histograms, but it could be that very high frequency noise has the opposite effect.
I've seen data sheets and appnotes that suggest adding series resistors or RCs to fast ADC inputs. I assumed that was to offset some charge injection thing, but maybe not. Those might be lowpass filters.
Has anybody run into this effect?