Jeremy… you’re awesome… here’s why.
I figured out this problem and hopefully other people can use this knowledge for their own projects and maybe someone coding FCP at Apple can take care of this.
I conformed my 23.98 After Effects outputs to 23.98 using Cinema Tools. I brought the newly conformed QT’s (both none compression and ProRes HQ) and rendered them in my 1080psf23.98 ProRes HQ sequence. They played back perfectly!
However, workarounds and extra steps are not my cup of tea, so I kept investigating what Cinema Tools was doing and figured out what the issue is.
FCP and AE handle “23.98” differently. If you render something out of AE at 23.98 you get a clip that is 23.98. However, if you render a 23.98 clip out of FCP, it is actually 23.976 (the official “23.98” time standard).
Therefore, THE WAY TO FIX THIS PROBLEM is to change your comp/render settings in AE or whatever non-Apple program you might be using to 23.976 instead of 23.98. Then, when you bring in the 23.976 clip into FCP, FCP is happy and when it renders, it renders it perfectly.
It would be very nice if this were not an issue and FCP knew how to correctly deal with 23.98 clips of the non-23.976 variety, but at least in the meantime, this is a viable one-step workflow. Plus, thanks to Jeremy, if the clips provided ARE of the non-23.976 variety, then one can use the extremely quick batch conform tool in Cinema Tools, which must change the header information to please the FCP gods.
-Ken Peltan