My 8-week old baby does exactly the same thing. It started when he was around 2 weeks old. The first time I put him down at night, he sleeps quietly and peacefully. Then when I put him down after his first night-time feed, usually around 2.30am, he'll make grunting and straining noises which can easily last a couple of hours. The noises keep waking me up but whenever I check him, he appears to be still asleep - although he does sound like he must be in pain!
I asked my doctor about it also and he confirmed that it was definitely related to the under-developed digestive system.
The good news is that I've definitely noticed an improvement in the last couple of weeks and I'm hoping by 12 weeks that the night-time noises will be a thing of the past!