- External feedback mode is selected and the internal clock ports (C0-C5) are not connected.
- Extclk1 has more fanout than the Extclk0 port, which is selected as the clock to be compensated for.
If both conditions are true, then the external clock compensation is moved from extclk0 to extclk1. However, this change does not affect the actual compensation of the PLL. When the PLL is in External Feedback mode, the compensation is identical between the extclk ports regardless of which extclk port is being compensated.
The Quartus II fitter incorrectly moves the compensation clock without checking for the extfeedback mode. As a result, the Quartus II software selects the default port of clk0 as being compensated. Since that port is not connected, the software selects the port with the highest fanout (extclk1 has more fanout than extclk0) to compensate and changes it to that port.
This will be fixed in a future version of the Quartus II software.