FCP, while it can ingest and work with AVCIntra natively, there are no sequence presents for AVCintra. So it might just need to be converted to ProRes, so FCP can understand it better. It's like...it's OK that it has to hang out with AVCIntra...but it prefers ProRes, that's like it's BFF! So it will only be cordial with AVCintra. And not play nice sometimes.
Shane
Little Frog Post
Read my blog,
Little Frog in High Def