The current code is focused on converting novels, and one of the steps it does is to delete every single page break in the pdf. It's trivial to stop this behavior by running from the source code (comment out one line), but there isn't any easy way to do this from the UI.
If you were feeling enterprising enough to run from source, which is not difficult then I could point you in the right direction.
Start here, and if you get past this step I can let you know what to comment out.
http://calibre-ebook.com/user_manual/develop.html
This might be something to look at as an option for the new pdf engine... Regardless, technical manuals and the like are never going to be converted very well.