Hi Ben,
Are you going from one OS to another by chance? I’ve had problems going from Mac FCP’s flavor of prores to a PC AE’s flavor of prores.
Can you just not use the re-renders from fcp due to the time it takes to render? If time’s not the biggest issue, I’d really recommend just using the ‘animation’ preset. I had the same frame skip issue before using no compression, and then went to animation, took some rendering but then was great.
Also, could it have anything to do with your playback? Like processor or rt settings?