Maybe he needs a routine? Maybe you need to give him a hug, but don't be emotional. Just a hug and a kiss on the top of the head and tell him you have to go to work (or wherever you go) and tell him you will be back in a bit and to be a good boy.
I start mine out by putting them in the crate and then leave for 2 minutes and come back in. I may do that 6-8 times in a day. I don't make a big deal when I get them back out, I just say hi and let them out. The next few days I leave them for 5 minutes, then 10 minutes and 20-30 minutes until I am up to an hour then 2.
I would try a routine and when you come home, just open the crate or whatever you have him in and don't make a big deal about being home. I hope you can get it worked out. No one wants their fur baby upset while they are gone.
Good luck.
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