Changes you make in the dr1000.ini are imported into the gconf registry of the device when you insert the card, but it will not create keys which are added to dr1000.ini but don't exist there.
By changing %gconf.xml files, you basically add keys to the gconf (XML based) backend directly. While this probably works fine when you don't make any mistakes, the proper way to do this is with gconftool (/usr/bin/gconftool-2). Using this tool, you can add new registry keys to the device.
See gconftool-2 manpage here
An even better approach is to edit the gconf schema file which holds the extension associations (somewhere in /etc/gconf/schemas), or - better yet - create a separate one for FBReader. When you "install" the schema file (#gconftool-2 --install-schema-file=FILENAME), the appropriate keys are created in the XML files in ~/.gconf/. In an ideal world, the installation of the gconf schema would be part of the application's install process.
Now, the next time you shut down the device, connect to USB or 'safely remove' the SD card, dr1000.ini is updated with the new keys. Mind that the schema file in /etc will be lost on installation of new firmware images, but the gconf registry itself (in ~/.gconf) will stay. In case you run into troubles, you can revert to the original gconf registry by choosing "Reset to factory defaults" in Settings/SD Card.