Are you powering the Ensemble or Symphony MkII On/Off just from the front power button, or cutting power completely such as via a Power Strip or Power Conditioner?
The Thunderbolt card in the Ensemble or Symphony MkII is separate from the rest of the circuitry of the unit. When you power off the Apogee via the soft button on the front, the Audio Device circuitry turns off but the Thunderbolt card remains active.
This is so any other devices daisy chained to the Apogee remain connected to the computer. If you power off the unit by fully removing AC power, pulling the rear plug or powering off a power conditioner, you may find that afterward you need to Wake this Thunderbolt card again, by reconnecting the cable to it so the card knows to look for a computer.
Follow the recommended power up method here: