When creating a queue in system-config-printer it doesn't parse /usr/lib/cups/backend/* for what backends are available. Instead it just blithely assumes that "Locally-connected", "Networked CUPS (IPP)", "Networked UNIX (LPD)", "Networked Windows (SMB)", "Networked Novell (NCP)", and "Networked JetDirect" are the only options, and are always available. This causes an issue if additional backends such as CUPS-PDF are installed because s-c-p completely ignores the additional backends.
This is as designed. Printconf needs throwing out and redoing from scratch IMHO.