I've seen quite a few fords myself have the same issue. My 97' Mustang has the same issue. It almost seems they baked the paint on too hard. As soon as a rock chips it, it begins flaking.
Generally speaking, I believe Ford's paint and corrosion warranty is good for 5 years. So, depending when you bought it, it's getting fairly close. If you can prove it's still under 5 years, you could possibly keep pressing the issue, but to tell you the truth, you may go through a lot of hassle and aggravation trying to get them to do better than 50% and still turn out that's all you get.
Good Luck either way.