Well, I base this all on what I've heard, but I believe the problem happens with multiple saving instances.
As far as the comments on the css, I would guess your source grouped the styles according to where they are used -- i.e. the "Title Page only CSS" will apply anywhere that class is used,
but it is only being used (theoretically) in the title page. And same goes for the ToC only css.
In other words, it is a suggestion that those styles should be used exclusively for formatting the title page. Some non-DRM'ed books I've gotten do similar things in the stylesheet. Personally, I would think there is greater clarity (and safety) in making three stylesheets, then linking each one where they belong, but who says life has to make sense?
Perhaps someone else will pop up here to elucidate the matter further. I just play with the books I've bought -- other people here (like you) do this for a living and have far more experience with Sigil.