Neither side was prepared to house large numbers of prisoners. For instance, Camp Butler (Springfield IL), Camp Morton (Indianapolis IN), Camp Randall (Madison WI) and Camp Douglas (Chicago IL) all had been used to train U.S. volunteers. Each camp had to be hastily converted to house Confederates captured at Fort Donelson and Island Ten.

http://freepages.history.rootsweb.ancestry.com/~indiana42nd/campmorton.htm
http://reocities.com/bourbonstreet/2757/issues/camp.htm
http://lincoln200.wisconsin.gov/category.asp?linkcatid=3206&linkid=1399&locid=156
http://www.waymarking.com/waymarks/WM37JC_Camp_Butler_National_Cemetery_Springfield_IL

Since both sides wished to have prisoners-of-war returned, a cartel was established to arrange for agreeable terms. The cartel remained in operation until the summer of 1863 when Confederate authorities objected to release of black prisoners. The agreement broke down at that point, and few exchanges took place subsequently until the final weeks of the war.

A few months after the surrender of Vicksburg, the Confederate government pressed most soldiers paroled there back into service. I'm not aware of anything similar following the Battle of Shiloh. What is your source for Jefferson Davis urging paroled Confederates soldiers to ignore terms of their release?