Ken,
I cannot say why the flag was attributed to an Alabama regiment. A 1913 book on Philadelphia regiments states that the 88th Pennsylvania took two flags, one from the 23rd North Carolina and the other from the 12th Alabama. Since the fate of the 20th North Carolina's flag is known, the 5th North Carolina would be the obvious alternative, but Orderly Sergeant James Peyton Britton of the 5th North Carolina is credited with wrapping that flag around his arm and carrying it from the field.