Modifications in the T-X meant that it was able to contact skynet in future via the telephone line so it was able to send skynet all information about john. I believe that because T-X and the early SKYNET co-existed in the same time period in T3; T-X was able to feed historical information about John and Kyle to SKYNET. Thus Kyle was already known to Skynet before he was even born. However, in T2, you will note that in one scene, Police records of Sarah and Kyle show that the the father of Kyle is listed as 'unknown'. So what gives?