Simulation using Quartus generated ibis models

Hi I'm using Quartus to generate ibis models for my circuit simulation in Altium DXP 2004. Using the simulation analysis to impedance match the signals and I find that 50 ohm series resistances will reduce the noise. I go and enable the 50 ohm output series resistances in Quartus on the troubled signal outputs and re-simulate. However, I get the same results!

The 50 ohm series output resistance I have enabled seems to have made no difference to the simulation results.

I've run through all the appropriate steps in the simulation, and spent many hours fixing/adjusting ibis models, double checked that specific pins are being assigned the correct models (input, output) etc...

Has anyone done this before? Any ideas why there is no change in my results? Suggestions of things I should check?

Thanks!!