Somebody correct me if I'm wrong, but I think that, per the spec, all external Hubs are supposed to support power switching on the downstream ports (and root hubs don't have to provide any power switching capabilities at all). However, the Hub spec does not necessarily require the downstream ports to be controlled individually -- all of the ports could be "ganged" together so that you must turn the power on or off to all downstream devices at the same time. If the device is self-powered, of course, manipulating the bus power should have no effect, anyway.
In addition, not all OS's provide a way to access to the power control even if the hub provides it, and the fact that a hub is supposed to allow power control doesn't necessarily mean it actually does.
I think the bottom line in your situation is that power control is the wrong approach -- I don't think you can count on it working 100% of the time.