The main reason is canonical violations during elections.
April 2, 2014. PRAVMIR. The Patriarchate of Constantinople has issued an official statement on the election of the new head of the Orthodox Church of the Czech Lands and Slovakia
The communiqué, in part, states:
1. The Patriarchate of Constantinople does not recognize the election of the new head of the Czechoslovakian Church, Archbishop Rostislav, following the resignation of Archbishop Christopher, “in connection with canonical violations during the election.”
2. Accordingly, any action of the Czech Church hierarchy is anti-canonical and will not be recognized by the Patriarchate of Constantinople.
3. The Orthodox Church of Constantinople “as the Mother Church, is ready to take an active part in resolving the problem, calling on both parties to continue negotiations and to avoid any actions that may aggravate the current sad situation in the Czech Church.”
In early March 2014 negotiations were held at the Patriarchal residence in Phanar between Metropolitan Simeon and representatives of Archbishop Rostislav, Bishops George and Joachim, yet the dialogue was unsuccessful.