We've had export issues with Ulysses. A Markdown export adds slashes,
and a Text export strips the formatting.
Once Markua is 100% complete, we intend to contact them and ask them to add
Markua support to the exports. Markua is an open spec, and hopefully
Leanpub will get it widely adopted enough that they'll add it.
In the meantime, here's a gross workaround.
First, write the document in one file, instead of in multiple files.
Then, instead of doing an export, do this:
Open the document in Ulysses.
Format > Make Plain Text (or Cmd + Shift + T)
This gets exactly what was typed, without it being mangled.
Note that pasting into another editor may or may not work. In Emacs
24.5 on OS X, trying to paste the text completely crashes Emacs.