In a blog entry by Alistair Christie I read about certain difficulties with the FrameMaker output from MadCap Flare. I didn’t even know there was such a feature… I had to comment on this:
So you want to do single-sourcing and want to have decent layout in PDF files? How dare you… 🙂
For single-source workflows I always recommend to start with a classic DTP application including page layout features. It is a lot easier to convert such documents into any HTML-based online format (by throwing away all those ›keep with next/previous paragraph‹, ›start a new page here‹, ›make a discretionary hyphen there‹ stuff) than the other way. Even the most advanced XSL-FO programming cannot forsee the intricate layout restrictions of a fixed page size (admitted: unless the layout is highly regular).
So, going from RoboHelp, Flare, or other online-help creation tools to print publishing is harder than going from FrameMaker (or Word, if you need a challenge) to HTML.
I am not surprised.