This is one of many, many forum pages I’ve read through trying to solve a very similar problem — being made to re-render after every slight change to every clip, making progress nigh on impossible. I had sequence settings exactly matching the clips I was importing, and was using reasonable codecs — same result with Apple Animation and Apple ProRes 422.
But then I solved it. 🙂
The problem was the non-standard resolution I was using (1440×900, screencasting my full laptop screen). As soon as I started recording the screencast clips at 1280×720, using ProRes 422, FCP started cooperating and was happy to manipulate the video clips as it should.
That’s two weeks I’ll never get back, but hey, I’m making progress now!