There is, of course, the "Cherokee Braves" flag at the Sweeny Museum (Wilson's Creek) though I have never found a period reference to this flag.
Lt Col Robt C Parks told Col D.N. McIntosh that their flag (of the 1st Cherokee Mtd Vols - Watie's) in Dec. 1862 was two red stripes separated by a white stripe and "nothing else". I'll find the exact reference but the description sounds like a first national without the field of blue.
A Southern Baptist missionary, whose name escapes me, describes two different white flags with moon and stars -- one may be the flag given to Pike in Tahlequah Oct 1861 and the other, very similar, carried by the Pins in July/August 1862.
What is known about the Choctaw Flag? The one in the OHS Museum.
There were also flags carried by the Texas troops (right?) that were the first national with 5 red stars for the Five Civilized Tribes. I assume this flag is what was given to Drew in Tahlequah by Pike in Oct 1861.
I'll post the specific text and source citations for the above when I get home tonight -- assuming the ice doesn't knock out my ISP.
Ken