This problem is most likely you aren't used to the position.
Some years back, I hadn't spent as much time on the bike, so riding the road bikes for more than an hour caused bad lower back and neck pain, where as they were perfectly set up. The issue was me not riding enough in that position. Once the miles were back up, I can ride all day without a problem again.
Road bikes do put quite a lot of pressure on an untrained back and neck.