Okay, so I backed it up, and ensured that "Ignore Margins" is still unchecked. (It was.)
An epub-to-epub was completely clean, it rendered just how I expected it to.
Epub-to-mobi, though: it's now respecting margin-left, but not margin-right or margin-top (the latter of which I've dropped to 0 because I want paragraphs during these passages butting right up against each other.)
So I'm still puzzled.