FWIW, I've grown accustomed to having to apply a First page manually in various situations; most often when I split a file into two, but also (I think) at least the first time I generate a ToC or LoF page. Completely off the top of my head, do you have any non-generated content (such as a title "Index") at the start of your generated index? considering the behaviour I'm used to from my ToC, this might be enough to "fix" your master page choice.
I do have a couple of text boxes at the top. Maybe that's what happened. Thanks for the suggestion; I'll check with the next book I re-build.