Do you live in the country? Is it possible your dog is hearing wolves, coyotes or coyo/dogs? I've noticed the time you mention is when packs in my area become vocal, although it never seems to bother my dogs. It's possible your dog is reacting to something only she hears, and I find wild canid packs are most vocal in late fall/winter/early spring. I often hear them around 3pm on cold, clear nights when leaving for work, it doesn't have to be a full moon.What DOES bother my guys is the presence of bears, fisher cats etc around the property. If you have lynx or cougar in your area, they really seem to stir things up.
Crate Training suggestions
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My wife and I have enjoyed the company of two B's over the last 3 years. They are perfectly crate trained to the point where they sleep in their crates with the doors open all night.
We've recently adopted a male foster B, and we are overjoyed at the new addtion to the family (the resident male B probably isn't at that point yet, though). However, we've noticed that our new B, a 10-month old, acts quite anxious in the crate. We suspect this stems from having been stuck at a Petland store in a display crate for more than 4 months before being purchased and consecutively owned by two previous families before coming to ours.
Any good tips on deconditioning the bad experiences of crating for our new B? We've got him going into the crate and sitting for a treat, but closing the door seems to make him frantic. We've left him in there for a few nights, but his constant anxious behavior has trained us to let him sleep with us. It's gotta end so when we travel, he'll be ready to sleep in a crate at night at the dogsitter's place.
TIA
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Check out our post on Miles: A Rescue – you might something useful.
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http://basenjiforums.com/showthread.php?t=921
Here's the link.