What type of failure are you getting SI or timing? What specific parameter? Have you loaded the corresponding waveforms into oscilloscope?
You might want to have a look at Mentor’s AppNote 10685 that explains the right debugging methodology.
I am getting fails on the SI. It fails on the Monotonic, DC Thresholds Multi Cross, and Vref Threshold Multi Cross. I will take a look at the oscope signal, but last I checked it seemed to have no issues. I will also take a look at the appnote. I will let you know what I find.
Notice that the CKE signal is, by default, assigned to the control signal group. Therefore, it is analyzed the same as the other control signals, with a PRBS stimulus and setup and hold margins calculated at every transition. This gives you a good variety of scenarios when the CKE signal might switch. If, on the other hand, you don't want to see that many transitions on the CKE signal, you can simply not assign it to a signal group. Then HyperLynx will ignore it. You can run interactive simulations if you like, and have full control of the stimulus and timing analysis.