A few things on your post if I may:
>>>It has always been my understanding that Confederate "army regulations" required regiments/battalions on the march and in line-of-battle carry only one color.>>>
The manual used by teh Confederates was the same one written for the US Army by William J. Hardee. Hardee based his manual on the French manual of the mid-1840s and that manual specified one flag for a regiment. This altered the older Napoleonic mode of one flag per maneuver battlion of a regiment - meaning from 2-4 flags per regiment (Napoleonic regiments were much bigger than Civil War regiments). Within the US Army itself, the flags had gone from 2 per regiment (Von Steuben's "Blue Book" of 1778) through Winfield Scott's manuals (up to three flags) and then back to 2 flags and then with Hardee's only 1 flag.
Hardee's manual was redone by Union officer Casey into Casey's Tactics and he reinstated the 2 flags per regiment basis which the Union Army used in the war.
There were a few times that CSA regiments did use two flags in the war - in particular when they were combined. At Chickamauga I have accounts of some of the combined Tennessee regiments going in with both flags and two color bearers.
We should be thankful, I suppose, that the British and Prussian armies of the early to mid-1700's dropped from 11 flags per regiment (a colonel's color, Lt. colonel's color, major's color and one for each company) to 2 flags and 5 flags respectively, and that we did not copy the Prussians but instead the British! Von Steuben was a Prussian!
>>>Regiments/battalions could have all of the individual and company flags they wanted while in camp, but on the march and in line of battle, the rule was only one.>>>>
Company colors pretty much fall of the charts after April, 1862. Most company flags had either been sent home or stored in wagons. Some did get used when regimental colors were lost and not replaced in time for the next battle.
>>>Records I have seen suggest that these two flags were provided by the same quartermaster source in the fall of 1863 while these regiments were still in central Mississippi.>>>
The Second national flag of the 3rd Mississippi of Loring's Division was made by one of its members - and I highly suspect that the other Second Nationals issued at this time were as well. They were easy to sew and any man with decent tailoring skills could make them. The 12 star Second Nationals did come from a contractor in Mobile - Jackson Belknap.
>>>The "one flag" boast by these veterans can not be true since the 12th Louisiana Infantry regiment was enrolled in Confederate service at Camp Moore in August 1861 three months before the "battle flag" (blue saltire on red background) pattern was adopted for regimental colors in Virginia. This pattern did not work its way west until General Beauregard showed up at Corinth in the spring of 1862, and I am not aware of any reords showing that it was used by any regiments at Shiloh. Issues of the St. Andrew's Cross pattern were made to the newly formed Army of Tennessee in the summer of 1862 while still in Mississippi.>>>
A couple of corrections: The flag that Beauregard wanted for the then Army of the Mississippi was the type of 12 starred saltire flag he had brought from Virginia. Accordingly, he ordered Polk's Corps to adopt them when they arrived at Corinth as well as Bragg's Corps who came up from Mobile and Pensacola. The shipment of these new 12 star flags (with 6 pointed stars) for Polk's troops got lost and did not arrive until after Shiloh. Those for Bragg's troops did arrive in time and they were indeed used at Shiloh where one of the Mississippi flags was captured on Day 1 and then retaken by the Confederates on Day 2. These flags were made in New Orleans by Henry Cassidy. Once Beaurgard had taken his sick leave, Bragg was not as adamant about making the Army of the Mississippi adopt the flag. Even at Shiloh, Polk's troops used their silk Polk Corps flags; Hardee's the blue and white flag of the Army of Central Kentucky (from which they had come) and Breckinridge's troops a hodge-podge of flags but mainly First Nationals.
Lastly - the Army of Tennessee did not come into existance until November, 1862. Before that they were still called the Army of the Mississippi.
>>>Assuming that flag standardization and uniformity was rigidly enforced in Confederate commands throughout the war, the 12th Louisiana would have been issued a Polk Battleflag circa February 1862, and a Van Dorn Battleflag in the summer of 1862.>>>
I agree with the issue of a Polk flag - one of the 45 silk flags made in Memphis, possibly by James Cameron in January, 1862. These were larger than the more commonly known second issue Polk flags (dating from the late Summer of 1882- wool with white edging between the red cross and blue field and 11 stars) and they had 13 stars and no edging between the cross and field.
I have doubts about them getting a Van Dorn battle flag however. First, the issue of these flags seems to be pretty limited to troops that had been in the Trans-Mississippi that had come over with Sterling Price and Earl Van Dorn. Secondly, some units that did not serve in the Trans-Miss. but were joined to the army, like the several Mississippi regiments, did get these flags. To what extent is the problem since there is little that we have found to date for the level of distribution. But it does not seem to be as deep as we had once thought.
The crescent of those flags is taken from the Missouri state Coat of Arms and was to inspire Missourians to leave their homes and fight east of the river for a time. The first issues of these flags were to what would be Cockrell's MO Brigade in June, 1862. The flags were made by the ladies of Guntown, MS and had fringed borders. The second issues of late August, 1862 were made probably in Jackson, MS by a local flag maker (whose name I forget offhand)and these had the more familiar star patterns and lacked fringed borders.
>>>>It has been a puzzle to me that flag captures from units of Loring's Division at Peachtree Creek include both St. Andrews Cross (I know Gregg - itís a saltire, not a St. Andrew's Cross!!) and 2nd national colors. >>>
Loring's Divison had been transferred with Polk's Army of Mississippi (later renamed the 3rd Corps, Army of Tennessee) to Georgia in May, 1864 from the Dept. of Alabama, Mississippi and East Louisiana. This department began to standardize their battle flags after Vicksburg when Joe Johnston was still in command of the department. he too, helped spread the saltire battle flags across the Confederacy. The first units to get the rectangular, 12 star battle flags (made in Mobile by Jackson and Sarah Belknap and James Cameron), wer ethe cavrly regiments of William "Red" Jackson's Division in October, 1863. An Alabama brigade got them next and it continued into July, 1864 when Forrest's Cavalry Corps finally got some.
So when Loring showed up in Georgia his regiments carried two types of flags - although not together in the same regiment.
Hope this helps.