I experience the same problem when I ride one of my Dutch granny bikes over any real distance. I am confident that the problem is the saddle position in relation to the cranks. The seat tube is very laid back. You're not really over the pedals, but mashing at them from behind.
The seat on my other Dutch bike has the seat clamp reversed and the seat is shoved forward on its rails. Much closer to a proper knee angle. No problems with pain on this bike. Thus, it's the one that I choose for any ride more than a couple of kms.
Try getting that seat as far forward as you can. You'll likely need to raise the post a bit when you do.