Yes, when using the Quartus® II software to generate preliminary IBIS models for Stratix® V, Arria® V, and Cyclone® V devices, the differential input models with differential OCT enabled will not work properly. This includes all differential I/O standards such as LVDS, mini-LVDS, and RSDS.
There is a DC shift on the received LVDS signals which affects the positive and negative signal crossing points making the model unusable.
You can place a 100 ohm resistor directly across the input pins of the differential receiver without using transmission lines between the resistor and the receiver pins. This will closely replicate the function of the differential OCT.
This problem is scheduled to be fixed in the final versions of the device IBIS models which will be available in a future release of the Quartus II software.