The things are going better (not quite)
With the version 0.3.1-0ubuntu2 the terminal's messages are:

/usr/lib/pymodules/python2.6/gnome_lirc_properties/net/services.py:23: DeprecationWarning: the md5 module is deprecated; use hashlib instead
  import md5, os, re, rfc822, sha, time, urllib2
/usr/lib/pymodules/python2.6/gnome_lirc_properties/net/services.py:23: DeprecationWarning: the sha module is deprecated; use the hashlib module instead
  import md5, os, re, rfc822, sha, time, urllib2
WARNING:root:/usr/share/lirc/remotes: Remote DVICO_MCE listed twice in dvico/lircd.conf.fusionHDTV and dvico/lircd.conf.fusionHDTV.
WARNING:root:/usr/share/lirc/remotes: Remote BESTBUY listed twice in bestbuy/lircd.conf.bestbuy and bestbuy/lircd.conf.bestbuy2.
WARNING:root:/usr/share/lirc/remotes: Remote NEC listed twice in generic/NEC-pulse.conf and generic/NEC-short-pulse.conf.
WARNING:root:/usr/share/lirc/remotes: Remote linux-input-layer listed twice in generic/devinput.conf and linux-input-layer-lircd.conf.
WARNING:root:/usr/share/lirc/remotes: Remote NEC listed twice in generic/NEC.conf and generic/NEC-short-pulse.conf.
WARNING:root:/usr/share/lirc/remotes: Remote SONY listed twice in generic/SONY12.conf and generic/SONY20.conf.
WARNING:root:/usr/share/lirc/remotes: Remote Hauppauge listed twice in hauppauge/lircd.conf.hauppauge and hauppauge/lircd.conf.hauppauge.
WARNING:root:/usr/share/lirc/remotes: Remote Medion_X10 listed twice in atiusb/lircd.conf.atiusb and atiusb/lircd.conf.atiusb.
WARNING:root:/usr/share/lirc/remotes: Remote Medion_X10 listed twice in atiusb/lircd.conf.atiusb and atiusb/lircd.conf.atiusb.
WARNING:root:/usr/share/lirc/remotes: Remote PVR2000 listed twice in leadtek/lircd.conf.PVR2000 and leadtek/lircd.conf.PVR2000.

The Auto-detect button now chooses "Apple receiver (0x8242)". The bottom message changed to :"Press remote control buttons to test: <none>", but the bottom message never changes, neither when any controller's buttons are pressed. 

With the new version there are no problems related with DBus. But it seems there are not communication with the controller and the program.

Maybe  these files could help to find where is the problem:
-- /etc/lirc/hardware.conf --
# Daemon settings required by gnome-lirc-properties
START_LIRCD=true

# Remote settings required by gnome-lirc-properties
REMOTE_MODEL="A1156"
REMOTE_VENDOR="Apple"

# Remote settings required by gnome-lirc-properties
REMOTE_DEVICE="/dev/usb/hiddev0"
REMOTE_MODULES="''"
REMOTE_DRIVER="macmini"
REMOTE_LIRCD_ARGS="''"
REMOTE_LIRCD_CONF="''"

# Receiver settings required by gnome-lirc-properties
RECEIVER_MODEL="Built-in\ IR\ Receiver\ \(0x8242\)"
RECEIVER_VENDOR="Apple"


-- /etc/lirc/lircd.conf.gnome --
# LIRC configuration file for Apple_A1156
# Generated by GNOME LIRC properties on Mon Sep 21 22:42:23 2009
# from apple/lircd.conf.macmini
#
# contributed by Sebastian Schaetzel
#
# brand: Apple
# model no. of remote control: A1156
#

begin remote
  name             Apple_A1156
  bits             8
  eps              30
  aeps             100
  one              0 0
  zero             0 0
  pre_data_bits    24
  pre_data         0x87EE81
  gap              211982
  toggle_bit_mask  0x0
  ignore_mask      0x0000ff01

  begin codes
    BACKWARD  0x08
    FORWARD   0x07
    MENU      0x02
    PLAY      0x04
    VOLDOWN   0x0D
    VOLUP     0x0B
  end codes
end remote


I wanted to check if lirc's daemon was working. I did the following:
$ sudo /etc/init.d/lirc stop
 * Stopping remote control daemon(s): LIRC                                                                                                            [ OK ] 
$ sudo /etc/init.d/lirc start
 * Starting remote control daemon(s) : LIRC                                                                                                            [ OK ] 

In the program the field Device is refering to /dev/usb/hiddev0, so I did the following:
$ sudo cat /dev/usb/hiddev0
�
 �
  �

�
 �
  �

   �
    �
     �

      �
       �
        �
         
          �
           �
            �


             �
              �
               �

               �
                �
                 �

                 �
                  �
                   �
                    
All these characters appear when a controller's button is pressed.