This is annoying.
You want to put a transition on some text or some images or video above the Secondary Storyline and it affects the Primary Storyline below. The screen goes black during the transition.
There are a couple of things to try here, and I suspect this is a bug that's triggered sometimes:
1. This happened today to me. Simply re-launching FCPX fixed it.
2. Try putting what's attached to the Primary Storyline into a Secondary Storyline. Highlight it, and all clips associated with it, say if it's a series of pictures or text, then hit COMMAND + G to put it into a secondary storyline. Apply your transitions and see if they only affect the upper Secondary Storyline.
3. Still not working? Try making the content inside the Secondary Storyline a Compound Clip but highlighting them all and hitting OPTION + G. Then dig into that compound clip by clicking on it's name/title/icon bar thingy (no idea what it's actually called, but it's the top of the compound clip, just below the "Shelf" of the Secondary Storyline) and you'll be inside that Compound Clip in another Timeline.
It's like a Nest in old FCP. Apply your transitions then tap COMMAND + LEFT BRACKET to go back to the main Timeline, the one the Compound Clip is inside of.
4. Still messed up? One last thing to try is to Right-Click on the Transition itself and look to see if you can toggle "Transition to/from Black". Usually it's greyed out though for some reason.
- You can Right-Click on a Transition in the browser and open a copy in Motion and try and edit it. I'll save that post for another day, though.