it really hurts, then it seems to go away, any ideas?
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You have probably got a mild case of plantar fasciitis.
What happens is that through the day your feet are sore and tight and hurting. But because you are walking around your circulation clears the bad inflammation chemicals that are building up around the area.
When you are asleep everything relaxes. Your body is usually prone (flat) so the chemicals build up. When you get up, there is tense, immediate pain because of the chemicals. When you walk around those chemicals are cleared.