They have the same meaning, but 'yet again' may suggest a certain irritatation or exasperation on the part of the speaker, implying that they consider the repetition of the situation to be somewhat excessive. For example, you would say that a certain very popular film star has 'once again' been nominated for an Oscar award. Your attitude to this could be either neutral or positive. However, if you say 'yet again' for the above situation, your attitude might suggest 'Oh no! Not again. Isn't it time to give someone else a chance?'. That said, there are many other instances where they can be used interchangebly, without any negative implications.