I doubt it is due to boredom since they get a lot of time out and about, but do you have any toys or chews in the x-pen? I feel like a lot of buns chew/shake the bars of their cages (or in your case attack the x-pen walls), even if they get a lot of time outside of their cage. Luna used to shake the bars of her cage at night, and eventually I gave in and after much bunny-proofing and trust-testing, I let her be out in my bedroom (her room) all night. But that solution is not for every bun, so you could try other methods. Unfortunately, other methods such as distraction (or water bottle spraying and coins-in-a-can shaking…I don’t condone either) require you to get up every time to address the situation, which doesn’t go over so well when you are trying to sleep! Is there any way to “tie down” the x-pen so they can’t lift it up?

I had the same experience. I let my rabbit roam everywhere for a long time yet she still chimed the x-pen. I couldn’t stand it haha! It could mean she wants to chew something as said above, and wooden chews would be a good alternative. Rabbits teeth never stop growing, so they naturally need to chew something. Another possibility is she is marking her territory. Probably unlikely but a sign of “you’re mine no one else’s” is when they chin things. So maybe it’s that?
What I did to stop this was upgrade to a different cage. It was larger but it was made out of soft materials that wouldn’t allow clinging and shaking.