Due to a problem in the Quartus® II software version 10.1, you may not be able to make edits to the analog settings tab for duplicated custom_phy or low_latency_phy instances in the Transceiver Toolkit.
To work around this problem, change the device family in the phy instance to Stratix® V and then back to the actual device family you are using. This will allow the analog settings tab contents to work correctly.
This problem is scheduled to be fixed in a future version of the Quartus II software.