The Vintage B3 organ is set up so that by default the sustain pedal is set to control the rotary brake, rather than sustain (since real B3 organ’s don’t have sustain pedals).
In order to change that you can open the Vintage B3 plugin, and then navigate to the “ROTOR CABINET” tab.
In the middle area, you will see “SPEED MIDI CONTOL” and by default this is set to “SusPdl Temp”.
All you need to do is change this option to a different one (for instance “OFF”) and then the sustain pedal will control sustain for the organ.