Longer NPT equilibration

I’m not sure exactly what compressibility that would make sense for biphasic systems. Have you looked in the literature? If you cannot find anything, I’d recommend a value closer to that of water than to cyclohexane. But you will have to decide the value of such parameters as you are the domain expert.

By the way, how many cyclohexane molecules do you have in your system? In a previous thread (Biphasic tutorial - #22 by SP06) you said you had a cubic 4.9 nm box with 218 cyclohexane molecules. In the tutorial there are 1114 molecules in a cubic 5 nm box. You might have so few molecules that it is taking unnecessarily long to reach equilibrium and the system is so small that it gets very sensitive to pressure and temperature changes. Make sure that your system is not too small (in both number of molecules and volume).