I can really sympathise. Elijah used to thump every night when I first got him and no neighbours complained but he was keeping me awake (possibly neighbours but they might not of known what the noise was) so I used to go out at around 2.00 am and fetch him in. I think it was attention seeking behaviour in his case. The accommodation inside was only temporary so I'd have to put him out again for space. Eventually he moved indoors when I had a swap round but if it just isn't feasible then you are at a dead end.
Elijah's hutch had thick carpet on the plywood but he still made himself heard!