Although I have selected the settings option to remove indents from first paragraph and after blank lines, when I compile my manuscript in rtf or docx format, all lines remain indented.
I know I could set these paragraphs the way I want them in the editor using styles, but this messes up my ebook formatting.
What tool are you using to inspect the output file? Word in particular can apply its own automatic formatting as soon as the file is opened, without necessarily telling you it’s done so.