Just so you don't feel lonely, I remember my XML::Twig project from a couple years ago, and I'd get the odd line here and there that didn't print out pretty. Which was ok - we only wanted it pretty for visual inspection, but it didn't get in the way of the actual use of the XML file as input to another process.

I do think that there is something funky going on in the pretty-printing of XML::Twig. That said, I'm glad that they concentrated on getting the XML parts working over the pretty-print!