I came across my first hybrid for which my 9000ES would not read the SACD layer: Bela Fleck's "Drive". It happens to be a MoFi disc; I recall at least someone else (maybe multiple people) on a'gon mentioning that the 9000ES has problems with MoFi's.
I tried the recalibration steps mentioned above, did the memory clear also before recalibration. Always had to do SACD calibration by itself; the unit never selected it from the "All" routine. Also, the unit would reject SACDs frequently; had the least success with discs that had multi-channel material (and were not hybrids).
Another MoFi disc I have works fine, one of the Kinks hybrids. Don't know offhand if I have any other MoFi hybrids, but I'll look.
I have had intermittent problems with a few other hybrids, but the unit eventually was able to read/play the SACD layer. I noticed that all of these offending discs were not pristine - scratches and/or smudges (how'd that happen!). I cleaned most smudges off a particularly finicky one with smudges and scratches, and it improved the 9000's ability to read the SACD layer. Fleck disc appears pristine, though.
I think I read in another thread, maybe on audio asylum, about the possibility of getting an updated laser assembly or similar for the unit. The thread mentioned model numbers for the original and newer assemblies. I'll have to find it again.