Pvt Edgar Warfield, in his book "From Manassas to Appomattox" after relating his units capture of two Union flagsx in the battles of Manassas and Sharpsburg says this:
"Incidentally, in the same museum (New York State Capitol Museum, Albany) is the flag taken from the roof of the Marshall House in our city on May 24th, 1861, by Colonel Ellsworth and in the same case with it is the colonels full uniform."

I emailed the curator of the museum and this morning received this nice reply with a short video of some of the conservation of this flag.

Dear Jim Baugh--

The Marshall House Flag belongs to the New York State Museum and was in display at the New York State Capitol last year and for six months at the State Museum through March of 2013. Currently the flag has been returned to the Military Museum and is being stored there. Here's the background on the flag from the Military Museum: http://dmna.ny.gov/historic/btlflags/other/CSA_MHF1995.3033.htm. Thanks for your interest.

Robert Weible
State Historian and Chief Curator
New York State Museum
>>> "surveypunk@embarqmail.com" 11/17/2013 1:09 PM >>>
Hello,
Is the flag from the Marshall House in Alexandria, VA, that was removed by Col. Elmer Ellsworth, 24 May 1861 still on display at your museum? Also interested in a detailed, dimentioned description of same and also any photos you may have of it.

Best Regards,
Jim Baugh

Appears to me the canton of the flag was constructed like in the drawing of the Marshall House at the beginning of the video with the stars being arranged in a 2/3 circle and not a complete circle.

JB