Dave, from the tone of your message, I assume you have not seen the web site, titled "The Steamer Autauga" at URL: http://groups.msn.com/AutaugaatWar/thesteamboatautauga.msnw which gives an account of this tragedy.
I can find no reference, in the Naval Official Records to this vessel. It was most definitely not a Union or Confederate Naval vessel, but was obviously a transport in the service of the Confederate government (see further details at the web site).