Separation anxiety can be extremely difficult to extinguish. Have you tried extending the intervals you're leaving? Five minutes, ten minutes, thirty?
Is there anything different on the days when he's calm vs. the days he's nervous? What about LL's suggestion to get him more exercise?
I'm wondering if you could find a cheap doggy daycare? I don't know if this would help with separation anxiety, but at least you wouldn't come home to a mess.
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