Thanks so much Eugene!

Using your advice I was able to see which pages have transparent images in them and either amend the images or just delete them.

2 things of note:

1. ID counts a rectangle – filled with colour and with a gradient feather applied – as a transparent image. I was using these rectangles in my headers so now they're just block colour with no effects.

2. Interestingly, ID doesn't like gifs or png files. It doesn't mind jpegs but gifs or pngs, regardless of what they are, seem to count as transparent images.

Why couldn't Adobe support just tell us this?

Thanks again.