If you set the transition time on light update in two separate commands to the same value, it never transitions on the second command. As a work around, I've been adding 1 to each command that is the same.
Example:
home.allLights.update(rgb: RGB_YELLOW_SUN, bri: BRI_RELAX, transitiontime: 29 * 60 * 10)
sleep(30 * 60)
home.allLights.update(rgb: RGB_ORANGE_RED, bri: 0, transitiontime: 29 * 60 * 10)
The second update transitions immediately.