Here's a well-researched description of flags carried by Breckinridge's Kentuckians during the war. Note that prior to Shiloh a Kentucky regiment received a first national design presented by the ladies of Huntsville AL. If the 49th Alabama didn't already have its own set of colors, it may have gotten a flag at this time. All these were replaced by Breckinridge's new design in May 1862. Those in turn were replaced by Hardee-pattern flags in March 1863. By this time the 49th Alabama Regiment had been detached as part of the Port Hudson garrison.

http://www.rootsweb.ancestry.com/~orphanhm/flags.htm