Have you found the problem? I’m having this same issue, where the brightness is different for a few frames around a cut. It only happens around some clips that are retimed. Thing is, they do it around clips that are retimed in FCP. I pulled the clips into Shake and output them, re-importing into FCP, and the same thing happens. I only see it when I watch a it in QT. It looks fine in Final Cut. Driving me nuts!
23.98 fps ProRes and imported Shake clips are 23.98 Animation codec.