There are many reasons why you would have a mix of new and old deck boards but it can be a common situation. The most frequent reason is that some of the boards needed replaced due to decay or wood rot while other board were still in good condition. It is also very common for a deck owner to protect the deck with a stain once all the repairs have been made. The dilemma is that new boards and old boards look very different when they are stained.
To understand why this happens may help you to minimize the problem. Once old deck boards weather the top layer of wood fibers begin to gray and become soft. Newer deck boards are denser and are very hard. The older boards will absorb more deck stain and appear much darker than the new denser deck boards which appear lighter.