"At Jackson [1904] there is in the "old cemetery" a plot of ground, separated from the other part of that cemetery by a chain; this is called the Confederate cemetery. Numbers of soldiers died of disease and wounds while the Confederate army was in Jackson and were buried there."

Source:
Confederate Cemeteries in Mississippi by R. W. Jones
Publications of the Mississippi Historical Society
Edited by Franklin L. Riley, Secretary
Vol. VIII.
Oxford, Mississippi
Printed for the Society
1904

The "old cemetery" in the excerpt above is the Greenwood Cemetery, the same Greenwood Cemetery from my first post in this thread.
http://history-sites.com/cgi-bin/bbs53x/mscwmb/webbbs_config.pl?read=18552

The soldiers buried here were probably marked at their death with wood markers and we know what happens with wood over time.