Why wouldn't it? The impedance isn't far off...
I wonder how accurately the line loss is modeled. You may have more HF loss than you're expecting. Though the waveforms look kind of "droopy", so it might not be too far off.
I would be more worried about radiation and interference around the ribbon cable: with an open transmission line like that, often the amount of signal lost in transmission, is lost to radiation rather than plain line loss...
(Importance of interference: 3V step into cable makes, say, -20dB --> 0.3V of interference. Multiplied by accidental resonances, at a Q of 10 perhaps, that's 3V potentially floating around which will interfere with other signals. Conversely, 30V (or for radiation, approx. 30V/m) of ambient interference will couple into the cable, corrupting logic levels.)
Best way to use ribbon cable is either as differential pair (which I would recommend), which gives you about 150 ohms differential impedance, and around 100 ohms common mode (if pairs are separated by ground wires: also recommended). Or for single ended signals, use alternating signal and ground wires (Zo ~ 100 ohms). Using lots of grounds (even when differential!) helps to reduce radiation / interference / susceptibility.
If you have lots of data, it may be reasonable to pack it into a Serdes (which I don't think the MAX will do natively, so will need an external IC; but the Cyclone may have one internal?), and use just one or two serial data streams instead of a ribbon full of parallel data lines. Then you can use, well, smaller cables certainly, but maybe something designed for high speed signals too (SATA?).
HTH,
Tim