It sounds like the IBIS component links these pins with a differential pair or a series model. Look at the two pin numbers. Find those pins in the IBIS file and see if they appear in the [Diff Pair] or [Series Pin] block, or maybe somewhere else outside the [Pins] section.
Yes they appear in the series pin mapping block. Actually the component is voltage level shifter (TI's LSF0108, IBIS). And the pins are actually in series, but if I comment out the series pin mapping and corresponding switching states, it works fine. Any idea why is it so?
I don't see anything wrong with the model file. I have used series switch models in the past, but not recently. The model should work fine in HyperLynx. Maybe you should open an SR on Support Center and provide the design data so we can find the problem.