Part of the problem is how each program (and reader) handles rendering. Stanza is known to strip CSS formatting whereas Calibre attempts to retain the CSS formatting. What really matters is how the indents were handled. Where they done with CSS, with rendering of standard elements, with , or with spacer gifs? It
might be something as simple as Stanza displaying <blockquotes> with indents as part of its normal rendering, whereas Calibre might not add any rendering to <blockquotes> unless specified by CSS ...
And even then there is no standard for how different (X)HTML elements should be rendered. Even with <p> tags, some browsers will place a blank line between paragraphs (business style), some will not but indent the first line of the paragraph (book style). Web designers have to maintain a full suite of browsers (as well as multiple versions of each browser) to test out their page designs simply because every browser insists on doing things its own way.
Even with the exact same mobi file, guaranteed that Stanza (on PC), Calibre, MobiPocket (on PC) and Kindle would each have a different rendering ...