Under the radar recently, both CIA Director Porter Goss and FBI Director Robert Mueller paid separate visits to Turkey. One of the main topics of both visits, according to a variety of sources quoted by Winds of Change, was Iran.
You may or may not be aware of this (I didn't know much about it), but Iran and Turkey are not exactly kissing cousins. Both are majority-Muslim countries, but that's pretty much where the similarity ends. While Iran is ruled by a radical Islamic theocracy, headed by their nut-job President Mahmoud Ahmadinejad, Turkey represents the other end of the spectrum; it is a secular, relatively democratic country that is actively seeking close ties to the West.
There's long been speculation that Iran sponsors a Kurdish-Islamic seperatist movement that opposes the Turkish government. And the development of nuclear weapons by Iran would scare the crap out of Turkey.
The Winds of Change article is a good read, giving a lot of in-depth information regarding the sore spots in the relationship between the two countries. There are quite a few of those.