I really believe it has to do with being sent hither and yon so many times during the war. During retreats like the one from middle Tennessee in the summer of 1863, another after the defeat at Missionary Ridge and of course the disaster at Nashville, many records were lost or destroyed. 5th Georgia records would have suffered on two of the three occasions named.
Another issue would be the high casualty rates you mentioned. When officers and orderly sergeants who normally handled records were killed or wounded, those who took their places may not have been familiar with standard routines. Wounded officers returning to duty often discovered that records hadn't been kept properly during their absence. After absences lasting weeks or even months, getting them up to date and back in order may not have been possible.
Another consideration would be the efficiency and abilities of John K. Jackson's staff. How many Confederate leaders can you name who were brigadiers prior to the Battle of Shiloh, but never considered for promotion over the next three years? This should tell us something about Jackson as a military officer, and may suggest that work done by his staff was less than stellar.