I'm having an issue with large blocks of text in Indesign: often times the last line of a paragraph will have an extra line space as compared to the rest of the paragraph. I've checked leading and all the other settings, they match the rest of the paragraph, but the line looks like the leading has been doubled. As I recall, this used to happen in Quark Express as well.
This is caused by the invisible return character at the end of the paragraph having a different size/leading to the rest of the paragraph.
Either use paragraph styles to ensure the entire paragraph has the same specs, or go to your InDesign preferences > Type and check the box labelled "Apply Leading to Entire Paragraphs"