Hello,
following the Stratix II manual, single-ended IO-standards as LVCMOS should be able to clock Fast PLLs. The restrictions applied by the fitter seems to be beyond device specification and thus a misbehaviour to be corrected. I was able to connect a global clock driving other parts of the design to Fast PLL input - with the aid of a clock control block instance.
Apart from what is allowed in the manual, it may be meaningful to use a differential standard anyway. Probably a pseudo LVDS signal made by resistive dividing of a LVCMOS clock is less sensitive to ground bounce than a ground referenced clock. At best use a real LVDS driver, e. g. a single gate SN65LVDS1.
Regards,
Frank