Rx_analogreset is not working properly when a Basic (PMA-Direct) channel is implemented in CMU channel of a Stratix® IV GX/GT or Hardcopy® IV GX/GT devices. This is due to a bug in Quartus® II 9.1 software. You may not see correct 'rx_pll_locked' and 'rx_freqlocked' behavior, as they do not respond to the rx_analogreset signal. The workaround is to use Quartus II 10.0 software. Regenerate ALTGX and ALTGX_RECONFIG Megawizard™ files, and recompile the design.