I'm having this problem too!
My female rabbit Delilah has been thumping almost non-stop for probably over 20 minutes now. Average 1 thump per minute but as many as once every 20 seconds or so. As far as I can tell, nothing set her off.
We keep her and my other rabbit Lahi in a 5x10 enclosure in the basement, with all the bunny amenities. But it's concrete floors! I'm seriously worried she might hurt herself thumping so hard. There's a pet crate with a plush pet bed in it and her giant litterbox and her cardboard hideaway for if she wants to get off the concrete, but she's not going in any of them.
Ah, I stand corrected, she just sat in her litterbox for a few thumps, then returned to the floor, and just now thumped again in her crate.
But nothing in particular happened before she started. I mean, I have my computer down here and I was listening to my online course videos, but that's nothing new that she's not heard before.
I went in to check it out. She's running to various spots in the enclosure, huddling a bit, and then thumping her foot a few times. Or thumping as she moves to the next spot. Her eyes are large and a little bit crazy looking. It's her dinner time and usually she'd be super happy about being fed but she's grabbing a few bites then returning to thumping. When I give her face rubs she calms for a bit, then dashes off again.
And this might be just her (she's an extremely vocal bunny, is constantly making chuckling sounds when she's busy and chattering noises when she's happy and growling noises when she's angry--she was raised by dogs and I'm pretty sure she never got the "rabbits are quiet" memo) but as she's thumping she groans first. So it sounds a bit like "myerrrrrhhhh*THUNK*!!" She's always done that as she thumps, but when she's non-stop thumping it's a worrying sound.
This isn't the first time it's happened but it is the first time it's lasted so long. The earlier suggestions of covering her hutch aren't feasible-- the enclosure is too big and is made of the house walls on two sides.
I'm at my wits end. She's acting and looking desperately unhappy. Our one rabbit Picca passed away two months ago, and while her brother Lahi has been depressed since then, Delilah was still in the process of bonding with her and didn't seem very affected. She started bothering Lahi too much (she was mounting him and in doing so was biting and pulling out the fur on his shoulders) so we separated them. Lahi's in a large cage within the enclosure so they can still see each other but not touch, so she might be getting lonely. Neither of them have been allowed out to run much as the basement's being reorganized and needs to be re-bunny-proofed, so they are getting a bit stircrazy. And just yesterday they went to the vet to have checkups and schedule a spaying for Delilah. They're both 100% healthy as far as the vet could tell.
She's been doing this more and more frequently. Does anyone know anything??