You may see the above warning message during Quartus II® Analysis & Synthesis of a design containing ALTGX_RECONFIG controller, if you have enabled the "Analog controls" option on page 3 of ALTGX_RECONFIG Megawizard™, but have not selected any of the Analog control ports (tx_vodctrl, etc) on the next page (4) of this Megawizard. Since, none of the analog ports are selected, it results in this warning.
The workaround to resolve this warning is to enable some of the analog control ports.