Well here is a picture of what I get graphing the data and then what the waveform actually looks like from the oscilloscope. I don't understand how you can get one from the other unless their timings were inverted. The other option could be that they're completely unrelated, but I find that hard to believe because all the min/max timings come out almost perfect when I invert the timings.
I have counters running with the waveforms and they're going up so it doesn't seem like the list file is inverted, just the values coming from the lvds receiver megafunction.