Did you choose to organize your transcript by subject? These subjects will be sorted alphabetically by default. If you prefer to sort them differently, simply click the "Add Course" link. The new course tray will open. Underneath the subject drop-down you'll see a tiny gear icon. Click this to open the subject editor. Click and drag on the black up/down arrows next to each subject to order them the way you like. Click "Save changes" when you're done. The subjects on your transcript will now appear in the new order you just defined.