I'm tinkering with the "tweak book" feature in Calibre, and I think I've found the problem - the whole book is not divided in paragraphs at all, the lines are just separated with two <br> tags one after the other. Calibre handles this, and the Opus too (though this might explain why it takes friggin' forever to open this one file), but CoolReader and FBReader follow stricter procedure and ignore the second <br> tag.
I'll try replacing the br tags with p tags and seeing what happens.
Edit: I followed
this suggestion, replacing all the br tags with p ones, and not only does CoolReader now work properly, but my Opus loads the file much faster. Victory!