An F55 can have a problem with an HMI the same way film can.
Silly questions first:
Are you shooting conventional frame rates and shutter angles?
Do you have the HMI ballasts in a suitable mode for what you're doing? Have you tried other modes, or adjusting frequency where it's adjustable? A lot of M-series lights will have the modern adjustable-frequency ballasts. If you do this be very careful that you don't introduce more problems.
Are both cameras running exactly the same firmware and with precisely identical configuration in all respects? Have you used a settings-transfer feature to move the complete settings stack from one camera to another?
Are you using any lens accessories such as a rain deflector, polariser-based variable ND, any other type of polarisation, or ND grads?
Are you using lenses with automatic iris or image stabilisation features?
Is there anything between the camera and the waveform? Is the problem visible on all outputs from the camera, both with and without LUTs?
Is there any mechanical fault with the ND filters in the cameras?
Are you using any advanced features of the Skypanels such as flicker effects, and have these effects been properly disabled?
Are you using DMX control on any of the lights, including HMI ballasts?
Have you tried moving the dimmer controls on the ballasts to ensure a dirty pot isn't causing the issue?
Is there any other light source leaking into the setup that may not be continuous, either at high frequency (old fluorescents, etc) or simply sunlight with a rotating fan in front of it?
Is the mains clean? Are any generators in good working order, not overloaded, etc?
Try using a cellphone to detect flicker. Hold it close to the light so that it winds down its shutter timing to a minimum, then watch for banding in its rolling shutter. This can be a highly sensitive test for flicker.
My guess: lights, probably the HMIs, but really you need to find a way to at least do the work to isolate this to a single bit of the lighting package, then replace or simply stop using it.
Skypanels are specced to shoot up to 25,000fps without flicker but I have not tried it and I am not, overall, that convinced by Skypanel as a product.
Also, when you find it, report back here so it goes into the collective consciousness.