The Allegro USB 3.0 card does not provide enough power for most USB 3.0 2.5" bus-powered drives and SSDs.
The Allegro USB 3.0 card powers bus-powered thumb drives just fine during wake, but does not have power for any bus-powered drives during sleep. In a Mac Pro, bus-powered drives will disconnect upon wake and need to be unplugged and plugged after sleep to reappear on the desktop. In a Windows machine, the drives appear normally after sleep. Wall powered drives do not have any issues with sleep in any machine.