This is a known bug in how we determine which bosses you have beaten. The game currently does this by comparing your high score on the event to the score needed to get a gold egg on the boss. For example, if the Chapter 2 boss requires 8,000 points for a gold egg, and if your high score versus the Chapter 2 boss is 8,123, then the game would realize that you've already beaten the Chapter 2 boss and must therefore be in Chapter 3.
The problem with this approach is that sometimes we change the score thresholds of the events' eggs, and if your score is on the other side of the new threshold then you'll find that your Chapter has changed. Continuing the example, let's say that we change the Chapter 2 boss so that the gold egg now requires 10,000 points. The game thinks that your high score of 8,123 is not sufficient to have beaten Chapter 2, and concludes that you are still in Chapter 2.
We should be fixing this issue in an upcoming release. It is *not* fixed in version 1.0, which had to be submitted to the app market well in advance of worldwide launch.