I've seen this problem on the list before, and it was always recommended to just pull the opacity down from 100% and it would clear it up.
Only it doesn't.
1. It may display correctly in the viewer, but will render wrong.
2. I can delete the overlay and put it back in - the problem is gone for a short while.
3. It doesn't always render it wrong - but my video has enough overlays that no matter how many times I try, it always does it to at least one of them.
I see the latest is 0.15, I'm rolling 0.13.5 (ubuntu std install). I'll try installing the latest from the website and see if it makes a difference.