Description
Yes, there is a known issue with Gen3 soft PIPE in Quartus® II software version 12.1 on Stratix® V GX devices. If txclkout is not routed through a global clock network, pipe_pclk will be inactive.
Resolution
To workaround this problem you should force txclkout to use a global clock with the following QSF assignment:
set_instance_assignment -name GLOBAL_SIGNAL "GLOBAL CLOCK" -to
"*sv_xcvr_native:inst_sv_xcvr_native|sv_pcs:inst_sv_pcs|sv_pcs_ch:ch[0].inst_sv_pcs_ch|sv_hssi_tx_pld_pcs_interface_rbc:inst_sv_hssi_tx_pld_pcs_interface|pld8gtxclkout"
This issue will be fixed in a future version of the Quartus II software.