an hour on the train isn't too bad, sometimes a bit of time apart, a couple of hours or a day not calling or texting can be healthy. You'd eventually go mad if you were hearing and with each other all the time, being apart is what makes the good bits feel better when you do get together, which you appear to still be getting from each other.
I'd back off and try not to give off any impression that you may be feeling insecure (nothing wrong with this, happens to us all) - past experience has done more harm than good for me here demanding clarification, it can scare the other person away. It's horrible though because it's always playing on your mind, the worst thing you can do is let your thoughts wander too much.
You say you haven't really settled at uni yet (again, been there at college, uni, new jobs, it happens) this can blow the other thing a little out of proportion (feeling irrational, a little needy) especially if you're not hearing from the other person all the time.
It's hard but try and settle down a little, make friends, enjoy uni, give him a little bit of space. He sounds like he still cares about you, this is the next step of the relationship (especially if you're an hour apart and circumstances have changed) rather than fearing the worst there's also signs in your post which indicate it could be getting stronger, even if you can't see them at the moment
now if only I could take my own advice