Hi,
You didn't mention whether you were nursing him when you go in at night "on auto pilot" or if you're taking him a bottle. I think sometimes it's just the comfort of the breast that they like waking up for :). My son has just turned one, and we started weaning him of the 1-2 night nursings he was still having, around 9 months old. When he woke up my husband would wait 10 mins to see if he'd settled back down, if not, he would go in with a bottle with a couple of ounces of expressed milk. The next night, if necessary, he would go in with water. After a couple/few nights DS cottoned onto the fact that mom wasn't coming in :), and he started sleeping through and was sleeping a solid 11 hours for ages.
Having said that, my son has started waking up again around 4ish. My husband travels sometimes for work, so unless he's home, I have to be the one to go in and there is NO WAY my boy will accept a bottle or just a cuddle from me when he knows my breasts are nearby. He is getting his molars in so I imagine that is what started it all, but can't be sure. However, honestly, I'm kinda ok with it. I figure if I let him CIO or whatever, I'm already awake, and feeling anxious because he's upset, and he'll just wake up in another hour and a half anyway and he'll be up for the day. If I nurse him at 4:30, it's still dark enough that he goes back to bed pretty easily (usually) and then we all get to sleep in till 7:30 or 8am! If I'm going to wake up anyway, I'd rather have the option of a better lie-in. I might live to regret it :), but I'm taking that road for right now.
Their schedules seem to be exactly the same - we also sometimes do a one nap day instead of 2 naps. It's a definite transition time. Best of luck to you!