Check the archives of this board, the Iowa flag has been discussed several times. The “Red Palmetto” flag is a pre-war pattern or pre-secession flag. Articles in the Charleston Mercury & Charleston Daily Courier describe similar flags. Also check Howard Madaus “Rebel Flags Afloat” again, his research on Secession flags. The “Palmetto” flag was also used outside of South Carolina as a flag supporting “Southern Unity” as far west as Nebraska.
The only conection to the “Citadel Flag” is the pattern. The flag in the Iowa collection taken during the Mobile campaign does not mean that it was captured at Fort Blakely since all of the forts around Mobile were captured about the same time. More then likly the flag was from a blockade runner in Mobile bay, it is to large to be a company or battery flag.
The Vincent family were not the only makers of secession flags. As to the position of the “Crescent Moon”, it faces all directions in other samples from the period. The proposed 1860 State flag the “increscent” moon in the blue union pointed upward, as did the first State flag 1861 through 1915. The 1915 State flag the points of the “Crescent Moon” pointed to the upper hoist. The 1950 through 1970 version the points of the “Crescent Moon” point toward the hoist. I believe the Iowa Historical Society still has a large South Carolina State flag captured in 1865 that the points of the “increscent” moon point upward (1861 flag act).
This question comes around about every two years, I believe Iowa has been notified of the new research on the flag, why they have not updated their files is unknown.