[Louisiana Infantry reenactors with Pelican flag, found on Google Images.]
"At 7:30 o'clock Sunday morning I received a verbal message from General Prentiss that the enemy were in his front in force. Soon after my pickets sent in word that a force, with artillery, were advancing on the Bark Road. In a very short time I discovered the Pelican flag advancing in the rear of General Prentiss' headquarters" -- Colonel David Stuart, 55th Illinois Infantry, commanding 2nd Brigade of Sherman's Fifth Division.
Why was not just one distinctive Battle Flag in use by Rebel troops at Shiloh?
In Alfred Roman's Military Operations of General Beauregard, page 171: "On the 28th November 1861 General Beauregard distributed to his troops (Van Dorn's and Longstreet's divisions) the new Confederate Battle Flag. During the Battle of Manassas he had observed the difficulty of distinguishing our own from the enemy's colors..."
But, there was "a problem getting the flag designed by Colonel W.P. Miles adopted. In the meantime, General Joseph E. Johnston ordered troops to carry State Flags until the issue of Battle Flag was resolved" (page 171.)
At Shiloh, a number of Union soldiers witnessed Louisiana troops bearing the Pelican flag in their attack on the Federal position.
References: http://archive.org/details/militaryoperati00romagoog Roman's Military Ops of General Beauregard, pages 170 - 3 and 481 - 3.
http://www.youtube.com/watch?v=WyPbKJJ9F5A "Alone on the Left: the Desperate Stand of Stuart's Brigade at Shiloh (part one) with Ranger Chris Mekow" video by Tony Willoughby and published by YouTube 7 April 2015. (See time positions 24.40 and 42.10 for mention of Pelican flag use.)
OR 10 page 257 (Colonel Stuart's Shiloh report)
Google Images for Louisiana Infantry reenactors with Pelican flag.