* Why do they appear to have difficulty finding a long-term CEO? Appointing the founder/CTO (edit: and after a long search and many short-term leaders) raises the possibility that either they couldn't find a willing external candidate or that there was conflict between the founders and the board. Which leads to ...
* Why do they appear to have difficulty finding board members? Even 5 seemed too few for such an important non-profit; to have 3 resign with only 1 replacement ready seems alarming.
* The PR of Eich's appointment, transition, and the political issue was poorly managed; Mozilla looked badly managed and the brand was damaged. The image of the organization is a responsibility for the CEO and, when hiring a new CEO, for the board. Even if the political issue never arose, losing a 3 of 5 board members when a new CEO is appointed looks bad no matter what public explanations are given. The appearance was that only 2 people supported the new CEO and one was his co-founder (again, appearances can be deceiving but managing them is essential).
These signs look worrying to me, but you'll notice that I wrote a lot about appearances -- I don't know the inside of Mozilla (I've participated at a low level for many years and have a sense of the culture and a few personalities, but that's all) nor do I know how to run a major non-profit or major open source project. Maybe someone here knows more.