I used to own a 2005 GT that did this from brand new. I drove it that way until the warranty was almost up and it never really got any worse. I tried replacing the valve stem seals and it didn't fix it at all. At the time I planned on keeping the car for a long time so I tore into it again and found it was the valve stem clearance was out of spec. I was surprised to say the least, as I've never heard this was a problem on these engines and have seen it on quite a few other cars. Ford's official stance was it was nothing to be concerned with. I went ahead and replaced the cylinder heads under warranty and it fixed the problem and I never had another problem with it. I do have to say I'm a technician at a Ford dealer, so I don't know if you would be able to get this covered on your car as I got the OK from my service manager to do the repair.
BTW, valve stem seals are definitely not a 1 hour, $20 repair on these engines. Pop the hood and it doesn't seem to be bad, but trust me, they are much more difficult than the 2 valve engines.
