Hi Garfunkle,
I am a dog breeder and a retired nurse turned Holistic. All this means nothing I'm just throwing it out there.
Dogs are very habit prone by nature once they get in the habit of a negative behavior it can be really tough. The important thing is to not give up. I read thru all the posts and did agree with posters Pass without a trace and wfurn.
The causes could be Barimetric pressure, earthquakes, fireworks or construction blasting. If its construction blasting that could going on for a couple of months easily. It might be worth checking to see if anything like that is going on within a 5 mile radius of your house.
Regardless of what caused it now the habit has to be broken. I assume you checked for spiders in the crate or bedding as well as tree branches scraping windows?
Did you know that dogs can also be afraid of the dark? So whatever is going on could be exacerbated by the fact that the dog can't see whatever is scaring him at night.
I feel that crates are a very good thing as long as they are not used as a punishment. My breed Rhodesian Ridgebacks are Den animals they use their crates to get away from things and get peace or as a hiding place so they don't have to share that special bone.
Here are a couple of things to try: Like the one poster said take down the crate block off certain areas and start fresh in a month. OR
Put the crate in a room that is in the center of the house with no windows if possible. (your trying to muffle noise) A bathroom with a ceiling fan would probably work best because then you have "white noise". Place a thick comforter under the crate so it does not have direct contact with the floor ie: vibrations.
Get some Rescue Remedy give that to him as late in the evening as possible. Preferrably keeping the dog awake till then also.
Get some Lavender Essential Oil. Pour a little in your hands rubbing it between your hands then massaging it into his coat. Put a little on his bed or blanket as well. Lavender oil is very soothing it helps dogs and people relax its used in Aroma Therapy. DO NOT USE ROSEMARY. Rosemary has been known to cause Seizures in epileptic and Seizure prone dogs.
I would put the dog in that room with his Crate left open. With one bed/blanket in the crate and one outside the crate. Close the door to the room or enclose it or block it off so the dog is kept in this area over night. *Leave the lights on.
You've now changed the location of the dog. The noise surrounding the dog. The dog is not in the dark. Also, the dog has a soothing aroma to smell with the Rescue Remedy helping to calm.
Hope this helps
