The problem with Turkey (and some others) is that they continue the massive violations of human rights and act in an agressive way today. Turkey now occupies Cyprus, violates the Greek and Cyprus airspace almost every day, and they have claims over the Agean.
1- The Turkish "occupation" of Cyprus has been continuing due to the Greek no vote to the Annan plan, which was appreciated by the UN and the EU.
2- Turkey claims that the borders of the airspace and others are not clarified through the agreements. I currently have no enough information, but I am sure this could be solved in the future. I came across to this statement at this website:
http://www.faoa.org/journal/gr-tu300.html
"Airspace. On the basis of a 1931 executive proclamation, Greece claims control of air space for 10 miles around its territory, to include its islands. In 1960, Greece agreed to a 6-mile airspace for NATO purposes, but since the 1974 Turkish intervention on Cyprus, Greece has protested whenever Turkey flies within 10 miles. These overflights often result in Greece scrambling interceptors and pilots engaging in mock dogfights."
There is a unilateral change of the policy by Greece over the extension of the airspace. Turkey sees this as a threat to its security. This issue should be discussed through bilateral agreements. However, the attempts by the Turkish government were rejected by the Greeks. If the Greek side was right 100% then the EU would warn Turkey and force Turkey to accept the Greek claims. But the EU saw this a problem between two sides and urged them to solve it by themselves.