3 mo. old dachshund puppy is quiet in crate for an hour, then starts barking

Our 3 mo. old dachshund puppy has gotten pretty good at being in his crate for about an hour to an hour and a half during the day. We’ve never had any trouble at night. He’ll sleep 8+ hours and doesn’t whine in the morning, he just waits until we let him out. During the day I’ve recorded him many times while away to see how he gets on. He’ll sometimes whine/bark within the first 5-10 minutes of me putting him in the kennel and leaving, but then he quiets down for at least an hour. Then he’ll start whining and barking, and will continue until let out(as long as 40 minutes of barking based on my recordings). I know I’ve accidentally rewarded it before by thinking he was being quiet when I came home, and then realizing from hearing the recording that he was barking/whining until he heard me coming. It’s frustrating because he’s so good for up to an hour and a half. I suspect he sleeps for that first hour to an hour and a half, and then starts barking and whining when he wakes up. What should I do? If I can approach quietly and hear him barking should I wait it out even if he goes on for at least an hour? I don’t know yet how long before he’ll stop again, or if he even will.

Thanks,
Ryan