Don't worry, we can fix it! It's not clean but it will work until you can update to a Paradise Arcade Shop LVT3 LED controller. On the 3 pin LED Board Connector, connect the middle pin and the pin closest to the start/select header. You can clip the wires and then solder/splice them together or even bridge the pins on the EZMOD board underneath. The LEDs should fire right up. Thanks to Megahurtz over at the SRK forums for being the guinea pig on this work around.
So why does this work? The stock LED board uses a transistor that is controlled by the stock PCB. The PCB sends a signal to the LED board (pulling the middle pin discussed above to +5V) which flips the transistor to "ON". The trick above constantly triggers the transistor making it always ON. Since the Brook UFB can't interpret any rumble data back from the consoles, this function can't be made to work and the LED board has to be left on or off at all times.