Also, if I apply any change on the misrendered layer, it resets. The problem might be solved then. But suddenly appear elsewhere on the timeline.
If I shut down AE, next time I open it, dorpouts might appear where they weren't before.
Do you still experience the issue if your .r3d files are on an internal drive instead of an external one?
I don't know. I have more footage than what can fit in my internal drive anyway...
Fair enough. Could you test it with a clip or two? I'm not suggesting this as a workaround, but a troubleshooting step.