By default, the Vintage B3 Organ only accepts MIDI input on MIDI channels 1-3. MIDI data with other channels (4-16) will be ignored. If the track's MIDI channel is set to a value above 3, the Vintage B3 Organ will not respond.
MIDI data on channel 1 or 2 plays the upper or lower Vintage B3 manual respectively. MIDI channel 3 plays the pedal. Set the MIDI channel of the Vintage B3 Organ track to a value between 1 and 3 to play one of the manuals or the pedal.
If you set the MIDI channel parameter to the default of "All", the MIDI channel of your MIDI keyboard or MIDI notes in regions on the track will be passed unfiltered to the Vintage B3 Organ. Choose this setting for a split keyboard or a dedicated organ keyboard setup. You can then set a dedicated MIDI mode in the Vintage B3 Organ window. You can change the MIDI channels for either manual and pedal by clicking the Split button in the Main window.
For further information on this kind of MIDI setup, refer to the Vintage B3 Organ section of the Logic Pro Instruments user guide.