To work around this problem, add the following assignment to your Quartus II Settings File (.qsf):
set_instance_assignment -name XCVR_RECONFIG_GROUP MERGE_TX_CDR_PLL -to "TX_Serial_Pin_Name"
set_instance_assignment -name XCVR_RECONFIG_GROUP MERGE_TX_CDR_PLL -to " <CDR/CMU PLL variation name>|altera_xcvr_cdr_pll_a10:xcvr_cdr_pll_a10_0|twentynm_xcvr_avmm:inst_twentynm_xcvr_avmm|avmm_atom_insts[0].twentynm_hssi_avmm_if_inst"
set_instance_assignment -name XCVR_RECONFIG_GROUP MERGE_TX_ CDR_PLL -to " <CDR/CMU PLL variation name>|*"