Hi @LoglinearSeal14 ,
I think it might have to do with how you are defining the X-axis (subgroup) in the P chart.
I tried this out with two different data sets from JMP: Orange Juice.jmp and Electrical Component Defect Screening.jmp.
In both instances, if you leave the subgroup X-axis "undefined" by not dropping a column in the control chart builder and then try to set the Ave or UL/LL to 0 width, then it removes it for all of the phases.
In the Orange Juice.jmp data sample, if you use :Status for Y, :Phase for Phase, and :Sample for Subgroup (X), and be sure to set to set it to Shewhart Attribute, you can remove a single phase's Ave and UL/LL lines, see image:
Similarly, for the Electrical Component Defect Screening.jmp file, if you use the CCB and set :N Defective as Y (be sure to select Shewhart Attribute again), use :Week as the phase and :N Units as the Subgroup (X), you can go in and set the width of the reference line to 0, see below (e.g. Week 10 has no average line):
I don't know if this is exactly the cause of your problem, but I have found some instances when you don't explicitly drop a column in the Subgroup (X) variable of the CCB, then this issue that you're describing can happen.
Without having your same data set and going through the same steps as you , it's hard to reproduce the error/issue/problem that you're having.
Hope this helps!,
DS