The earliest detailed descriptions of Shivaji's birth and boyhood are found in the works composed 150 years after his death. By this time, Shivaji had become a semi-legendary figure, and several stories had developed around his legend. Historian Jadunath Sarkar notes: "The stories told in the later Marathi bakhars about the history of his parents during the year preceding his birth and the events of his own life up to the age of twenty, are in many points contrary to authentic history, and in others improbable, or, at all events, unsupported by any evidence.
The exact birth date is unknown for the same reason. Any claims about his fathers whereabouts 9 months before his birth are likely to be grabbed out of thin air.
But I live in Maharashtra and here from many of people I have heard that when Shivaji was born, Shahaji Bhosale was in South India for last 3 years fighting war. And many of them say that As james Laine said, Dadoji Kondev is his biological father. So I think a real investigation should be made by government about this.