Well it turns out that for some reason, when final cut relinks the files, it converts my original 1280 x 720 clips to 1920 x 1080 clips.
I checked the original file, and the scales, and they were the same as before, but when I switched the Spatial Conform from “Fit” to “None” it completely fixes it.
Thanks a bunch. You’ve really helped me with this one 🙂