Physiological issues, qty and quality of sleep, diet (should snack every 2-3 hours), hyrdation (the brain is mostly water), air quality...
I would also suggest having a read of steves article on relaxifying your workspace.
From what you have said however it does sounds very much like an emotional thing. A lot of people call the first hour of the day the rudder. I find if you can spend the first our of the day getting a touch of exercise, leisurely breakfast and generally feel good for that hour, the rest of the day just gets that little bit easier.
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