Thank you dtietz and PrefectD for the responses.
I had a look in the floorplanner and it seems as though Quartus is using PLL1, as I expected. However when I assign the clk pin to the output pin of this PLL I continue to get the warning.
I´m sure its something simple, I´m out of the office for a few days so I won´t be able to work with it, but early next week I´ll have a proper read of the documnetation to see if anything is specified there. I´ll post whatever solution I find but in the meantime if anyone has been able to resolve this issue previously please let me know.
Thanks again.