I got into contact with a Wisconsin museum that has five confederate flags and inquired if they knew about their state flags that were captured in the war. I met with some success, here is what one of the workers supplied to me. Keep in mind that as they is being typed they are dismantling their furniture for improvements, but here is what they gave me and a link to find more on our own.

1st Wisconsin Cavalry flag, Regimental, captured at Varnell's Station,
GA, 9 May 1864 by Corporal Tom Goodman, Co.C, 3rd Arkansas Cavalry; the
upper part of the staff was shot away in the battle. V1964.219.5

8th Wisconsin, company flag, captured at Holly Springs, MS December
1862. Recaptured by Thomas Paul, Co. K 11th IL Cav. This flag is shown
on the battle flag website, under 8th Wisconsin. V1977.6

21st Wisconsin flag, Regimental, captured at Chickamauga, returned to
Wisconsin in 1905. V1964.219.103 (this identification is somewhat
debatable)

26th Wisconsin, Regimental, lost at Gettysburg to the 12th Georgia,
every color guard killed or wounded. Flag was never recovered or
returned.

36th Wisconsin, National, captured by the 44th North Carolina at Ream's
Station. Flag returned to Wisconsin after the war. V1964.219.158