Try adding a boring elliptical galaxy to the tutorial to see if its synthetic photometry is also biased in the same direction as the emission line galaxy example. This will be diagnostic: if the boring elliptical is similarly biased, then we might be doing something wrong; if the elliptical falls on the other side of the 1:1 line then we might be seeing the effect of weather, for example.
If that doesn't work, let's try investigating the data quality flags. Each sloan observation comes with a multitude of quality information which we might be able to use to identify more/less photometric nights.
Try adding a boring elliptical galaxy to the tutorial to see if its synthetic photometry is also biased in the same direction as the emission line galaxy example. This will be diagnostic: if the boring elliptical is similarly biased, then we might be doing something wrong; if the elliptical falls on the other side of the 1:1 line then we might be seeing the effect of weather, for example.