Greg,
I would suggest rereading Colonel Warren's promotion recommendation letter of 29 March 1864. I believe he is very specific about the flag (colors) which Gabriel Shank carried and when.

Warren wrote "Soon after the first battle of Manassas he was at his own request appointed Color-bearer of his regiment and has carried them in every action in which the regiment has been engaged. . ." Warren referred to ONE flag (colors).

Warren wrote "at [Chancellorsville] finding that he was about to be captured he striped the Colors from the staff. . ." Warren again referred to ONE flag (colors).

Warren wrote "His first flag. . ." Warren again referred to one flag (colors).

The flag (colors) to which Warren referred throughout the letter was Shank's first flag (colors). This flag was the Virginia flag presented by Governor Letcher to Lt.-Colonel Warren at Centreville (Colonel Gibbons was absent sick at the time.)

Warren also wrote that the first flag was "litterally shot to pieces". Of all the flags which can historically be attributed to the 10th Virginia or its companies ONLY the Virginia flag presented to Lt.-Colonel Warren by Governor Letcher at Centreville, and now on display at the Harrisonburg-Rockingham Historical Society can even remotely be described as shot to pieces.
1. 1859 Horstmans Brothers Pre-War flag: This flag was presented by the ladies of Harrisonburg to the Harrisonburg Valley Guards (later Company G) in September 1859. It was described as "an American flag, with 34 gilt stars on one side, and on the reverse side the Virginia coat of Arms, painted in handsome style." This flag was converted into a Confederate 1st National and carried by the regiment at Manassas No. 1 and 'reportedly suffered a cannon shot to the canton'. However, when I inspected the flag at the Harpers Ferry facility the flag was obviously NOT shot to pieces and the staff member, Nancy Hatcher, informed me that the damage to the canton was almost certainly due to age and improper storage. Additionally, H. Michael Madaus confirmed this regarding the canton in a letter of 26 June 1985. Also, while members of the 10th Va mentioned singing shells, whistling balls, exploding shells, what men were shot and identifying where, and men stabbed, not ONE man mentioned any damage to the flag. This flag was donated to the NPS in 1956 by a Gibbons descendant.
2. 12 Star Silk Flag: This flag was donated at the same time as the flag above. The card on this flag (catalogue no. 1004 accession no 108) describes this flag as faded. However, it makes not mention of any damage. Unfortunately, this flag is now missing.
3. Bunting ANV battleflag with orange border: This flag was captured by the 68th PA Infantry at Chancellorsville. Very little damage is evident on this flag; it was not shot to pieces.
4. Four-pointed Star rectangular battleflag: This flag has been attributed to the 10th Va but has no real historical evidence to substantiate that claim. It is marked as being presented to the regiment by the ladies of Harrisonburg in 1861. That is obviously a mistake and there is no surviving record of any member of the regiment referring to this 'presentation'. Regardless, there is very little damage evident on this flag.
5. "Home-made" Battleflag: This flag only survives in two know photographs. One photograph is in a history of Rockingham County; the other photograph is of Lt.-Colonel Martz and another man holding the flag post-war. Inspection of these two photographs show very little, if any, damage to the flag. No historical information seems to exist concerning this flag.
6. Virginia State Flag: A Virginia flag is on display at the Chancellorsville Visitors Center. It is identified as having belonged to the 10th Virginia. It did, in fact, belong to the regiment but is NOT the flag referred to by Colonel Warren as being shot to pieces. Some men of the regiment viewed this flag at Mrs. Geil's home in February 1896 and reported it was a battle-stained flag with some eight to ten minnie ball holes. Not what anyone would describe as shot to pieces.
7. Battleflag with honors: This flag shows some damage but not what one would refer to as shot to pieces.

As to disobeying orders, I believe that the original post in this chain from Neese about the Virginia flag makes a statement to that. Here was the 10th VA under the command of Colonel Gibbons having entered Jackson's command carrying a flag which after the issue of the silk battleflags was not supposed to be used. Again, the regiment flaunted the Virginia flag in 1862 when the army crossed into Maryland (refer to my previous post). And General Jackson was sitting right there and obviously saw it.

John