Is there a known problem with how the Intel® Quartus® Prime Pro software implements Differential SSTL and HSTL I/O in Intel Stratix® 10 devices?

Yes, due to a problem in Intel® Quartus® Prime Pro software versions 17.0 or later, Differential SSTL and HSTL inputs may not sample the input signal when implemented on bi-directional I/O in Intel Stratix® 10 devices if the respective VREF pin is not connected to a voltage reference. Differential SSTL and HSTL inputs should not require a VREF.