There are 2 or more main problems with the Josephus passage that really should be considered when trying to use him as a reliable source as evidence for a historical Jesus.
1st: He was not even a flicker in his momma's eye when Jesus is purported to have walked the earth, so everything he wrote was hear-say on this subject, or was copied from other sources, that he himself would not have used.
2nd: He hated Christians, he despised their actions, to him they were more or less heritical and would never haved considered anything that Jesus did as "Miraculas". If he did know that Jesus performed miracles then why did he not convert, he was a Jew, and never felt that Jesus was anything of any concequence. Infact, he wrote about more then one "Christ" and really considered them all false, including Jesus of the bible.
Much of the history, prior to his birth, was copied from sources such as the bible (OT) and not much from secular sources, so often when he writes of things such as the flood and the heritage of the Hebrew peoples, he is really recanting the traditions that were set forth in the scriptures, not secular writings that other nations and peoples had written, outside of the OT. If I recall, he even relied on some of the Apocryphal writtings such as Barach and Enoch, just to name a couple.
Seedy