Your Stratix IV GX device transceiver design fail to merge TX PLLs in the Quartus® II software if the TX PLLs within the ALTGX Megawizard Plugin Manager to be merged do not have identical parameters.
For the Quartus II software to merge TX PLLs, the settings, configuration, and inputs of those TX PLLs must be identical.
Examples of TX PLL parameters that must be identical for successful merging are: clock inputs, control inputs like reset and powerdown, bandwidth settings, dynamic reconfiguration settings, PLL type.