What brand of powered hub are you using? I had the exact same problem you describe using a D-Link 7 port UBS hub. I switched to a Belkin 7 port hub and the problem disappeared completely. It has not returned. I now have two Belkin hubs connected to my 24" iMac and no problems.
Bottom line I would bet your problem is caused by the hub you are using and not OS X
Is there a way to do this? I've found that periodically certain USB devices, particularly those connected to a powered hub, are not recognized by OS X after a restart. They require being physically unplugged and replugged. This problem is much worse with Snow Leopard. 100% of the time an Apple USB Modem has this issue and frankly it's driving me a bit nuts.
Interestingly the USB Modem in question _is_ listed in System profiler. However it does not appear as a recognized modem in /dev/ and so it won't appear in modem software like dialers, caller id, etc.
so the question is, is there a terminal command one could issue to force a rescan of usb devices?
or any other likely solution to emulate unplugging and replugging them?