This is due to an efficiency issue with the MIG pin allocation algorithm that prevents available pins from being selected for System Clock.
To work around the problem, follow one of the provided solutions:
- For Single-Ended System Clock designs:
- Select Differential System Clock.
- Choose available Pins in the "System Signals Selection" page for the System Clock and generate design.
- Comment out the unneeded System Clock pin in the generated UCF since single-ended is only needed.
- Change the top-level parameter INPUT_CLK_TYPE and set it to "SINGLE_ENDED".
- For Single-Ended or Differential System Clock designs:
- Generate the design using the "New Design" option without selecting pins for the system clock pins.
- Regenerate the design using the "Fixed Pin Out" feature and import the UCF constraints from the previous design created.
- Then, select the system clock pins and regenerate the design.