I had a similar problem with my car - before a tree demolished it and solved the problem.....but what I was about to replace was: the IAC valve (either get a new intake manifold from a junk yard or ebay or just the valve off of some place like eBay as the sensor from anywhere else is like $300). And then the main relay was always in the back of my mind.

I wish I had a for sure deffinate answer for you, but it was very odd for me too. It may also have to do with the fast idle thermo valve, that is my best guess actually from what you say about it going away after it warming up.

- Nathan