Hey you guys are welcome to download and look at the data... I linked it in my first posts. The more eyes the better!
Mike, I thought along those same lines, that there might be a pedestal in one or more of the flats, but there definitely isn't one listed in the header, nor can I detect one through any analysis I and a few others (David Ault being one) have done.
Rob, actually, it does seem that there are a few hot pixels (this is a very clean Sony camera, BTW) but those same hot pixels are in all of my flat data, and for some reason this data set is the only one that has the problem. But you might be on to something with that.