Yyyyyyeeeeeeessssssss..........
I'm not sure I'm on the same page as you, Ken... so there's probably something to learn here...

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I normalised the spectra to validate the comparison. Both spectra agree quite nicely except for the Ha line, which tells me the Ha line is saturated - at least in the 8s exposure. I would expect that the nonlinearity comes in as soon as some of the pixels in the image of the Ha line become saturated.
I don't follow how to compare the values in the raw spectra, because that's a product of the binning process, not just the ccd.
I've attached a comparison plot of the raw spectra. Both are scaled to Ymax = 340000. The peak intensity for the 4s exposure is 251035, and that for the 8s exposure is 309404.
I find the histogram in IC capture doesn't give a good indication of the saturation of such a small section of the whole image, hence the experiment to try to find the limits of linearity so I can ultimately compare spectra and intensity changes over time.
I've also included the zipped spc files if anyone wants to play.
Let me know if you think I'm off the rails...
Al.