What you are actually looking at is the difference between juvenile pecan leaves (the red ones) and sexually mature leaves (the green ones). If you look carefully, you can see that catkins were produced by the the sexually mature scion.
Seedling pecans must grow through an extended juvenile stage before they become capable of producing catkins and pistillate flowers. This juvenile stage usually lasts between 15 and 20 years. Juvenile pecan trees produce leaves and rachises with a noticeable red tinge. Leaves of juvenile trees also tend to be more pubescent (hairy) than leaves of mature trees.
When grafting a tree, we place a sexually mature twig (the scion) on a juvenile rootstock. Because the scion is sexually mature, the shoots growing from that scion will be sexually mature. This simple fact is the reason grafted trees start bearing pecans at such an early age as compared to seedling (not grafted) trees.
After taking this photo, I pruned all the trunks sprouts (red leaves) off this tree to focus all the tree's energy into the scion. I also attached a bamboo stake to the trunk, pruned the scion to one shoot, and tied that new shoot to the stake. I've got more grafts to trim tonight but so far the 2014 grafting season looks to be a 100% success year.