Mine never did remember settings when set via the Nautilus "open with" dialog. (I was trying to make VLC my default player for various video filetypes -- AVI, etc -- and it never stuck.)
I eventually got the setting to stick using Ubuntu Tweak's File Type Manager.
sudo add-apt-repository ppa:tualatrix/ppa
sudo aptitude update
sudo aptitude install ubuntu-tweak
Afterwards, Ubuntu Tweak should be available in your Gnome menu: Applications > System Tools > Ubuntu Tweak. Select File Type Manager in the left-hand column, select a filetype category, select a filetype, click the Edit button. There you can select from your system's known choices, or use Add to add a new choice or custom command.
See Adding MIME Types in the Ubuntu Help pages. To make a new MIME type, you can simply add the type to /etc/mime.types and the icon to /usr/share/icons/gnome/*/mimetypes (put SVGs in ...gnome/scalable/mimetypes, and PNGs in the size directories).
There seems to be a way to make this slightly more automatic via XDG. You can use the xdg-mime command to query what your system knows about MIME types and add new ones. See man xdg-mime; install the xdg-utils package if you don't have this command.
If your PPF files are just plain text, you might be able to get away with adding "ppf" to the existing text/plain definition in /etc/mime.types:
text/plain asc txt text pot brf ppf
