Compositing: Opacity - randomly making fade ins to clips

I'm on my fifth FCPX project. This one is a simple two camera shoot of an event - a dance competition. I set up my A camera as the primary storyline, my B camera (which I only shot for the actual dances) as b-roll. Not a secondary storyline, per-se.
When it came time for finishing, I wanted to Overwrite to Primary Storyline to simplify. When I did, I found random fade ins appeared all throughout the project. Always fade in, never fade out, and very inconsistent.
Very annoying to have issues like this at the final stage. QCing becomes a nightmare.
Thanks -
David

MikeAiken wrote:
...what's the absolute best format to export these intermediate files as full 1920x1080 to avoid as much recompression as possible?
Others have answered your direct question. The implied question is about workflow and how to maintain maximum quality. One way is to avoid making an intermediate.
You don't have to work on your footage in separate projects. You can work on separate sequences inside one project. If you do this, you avoid having to create an intermediate and maintain highest possible quality.
What I've done before in similar situations is to create subclips and then create another sequence and work on those subclips there. The subclips reference the original file non-destructively as is PPro's way, so maximum quality is maintained. When you're done adding titles, transitions, audio work, etc. then you just export this sequence just like you normally do.
PPro is a huge and complex program, and there are usually many ways to accomplish the same task. I'm only bring this up as an alternative way of accomplishing this task on the off chance you hadn't thought of it. Clearly, YMMV.

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