John, as Hugh so correctly stated the prisoners were required to sign the oath before being released. The site that you mentioned was set up and run by Ms. Perkins who has done an outstanding job with her board. The reason why these soldiers refused to take the oath was that the War was still going on in Febuary and March of 1865. So of course they would have stayed in prison. To be able to join the Federal military would have required the Oath (swallowing the eagle) as some liked to call it in that day. Also keep in mind that many more former Confederates joined the Federal military after the War but did NOT do so until the War had ended. I would think that their reasons were probably due to steady work and wages.