Hello bcao,
i know this warning.
In your device you have 4 PLL's.
One in every edge of your device. (Look into the Chip Planner).
Every PLL has dedicated clock input pins and output pins. (Look into the Device Handbook).
If you use one dedicated pll clock output pin to your external Memory, you
must check whether the associated pll is selected by the fitter.
If not, you can use the assignment editor to make a location assignment for the used pll to correct this.
See Attachmend.
In my case, after the location correction, the warning was gone.
I hope I could help