The Quartus® II software versions 6.1 and 7.0 remove global assignments to transceiver clocks when transceiver channels are merged, so some clocks may be assigned to local routes. The Quartus II software should promote the transceiver clocks to global or regional clock routes.
This problem has been fixed beginning with the Quartus II software version 7.1.
Alternatively to work around this issue in the Quartus II software version 6.1, install the appropriate patch from the following list: