The thumping could have been from that, but if they hear or smell something strange, that can also set them thumping. Some rabbits do like a routine, so that might help. When you are home make sure you spend some time with him, and if he likes to be petted, do lots of that, then when you aren't able to be with him, he may deal with it better. Also leave lots of toys and things for him to do while you are gone like cardboard boxes to chew on, phone books to rip up, you could make a digging box with shredded paper, rabbit safe wood chews. Rabbits usually sleep all day and are most active in the morning and in the evening. So that's when he will be wanting some interaction. If you get him neutered you could get him a bunny friend. That would help a lot, if you are able to find a pal that he likes and gets along with, but they would both need to be fixed for that to work.