Clips not sitting on top of each other in FCPX This may sound odd but I'll try and describe it properly.

I have my main video in the timelime all ok, I then drag in a picture on top of that, or possible a compound clip of multiple pictures, still all ok.

I then drop in another image on top of that compound clip/first image (possible an element like a shape).

Sometimes when I drop something in rather than the clip sitting on top of the clips underneath it like normal it drops into the same line as the clip underneath and is not visible, I try removing the last added object and re-adding but it doesn't work, usually the only way round this I've found is re-adding the clip underneath that the above clip is falling "into" if that makes sense?

All clips (barring the last one thats dropping into the clip below it) are visible in the video fine, am I accidentally setting a property on that clip item with a random accidental key press somehow?
Sounds weird. Maybe try deleting the FCPX preferences: 

Hold Command Option and start FCPX. A window will pop up and ask you if you want to delete the preferences.