Yes, a known issue exists with the transceiver rx_eqdcgain PMA control in Stratix® IV GX and Arria® II GX devices.
The rx_eqdcgain value of all channels within an altgx MegaWizard® Plug-In Manager instance are overwritten by the rx_eqdcgain value of logical channel 0.
The issue is seen when both the "Use 'logical_channel_address' port for Analog controls reconfiguration" and "Use the same control for all channels" options are disabled in the altgx_reconfig MegaWizard Plug-In Manager.
This issue affects Stratix IV GX/GT, Arria II GX and Hardcopy® GX devices compiled in Quartus® II software versions 9.1, 9.1-SP1, and 9.1-SP2.
To workaround this issue select either of the following options in the altgx_reconfig MegaWizard Plug-In Manager:
"Use 'logical_channel_address' port for Analog controls reconfiguration"
"Use the same control for all channels"
This issue will be fixed in a future version of the Quartus II software.