Hi!
Recently i encounter same problem, i.e., exactly, no power on all USB ports *after* shutdown. The power presents before OS start (when only +5VSB present), and work when motherboard fully up, but lost when OS shuts down.
Firstly i look for well known 5V <-> 5VSB jumpers, but none found on my board (exactly photo is here http://www.robiecomputerparts.com/images/M_asus%202.jpg). Then i walk through BIOS setup settings, but none relevant was found. I do not try to change S5 to S3 state or so, because i never wish to power additional unneeded parts of computer for the price of only powering USB pwr pins.
I do not have Windows OS and do not have any idea how to use any tweak utilites or/and drivers provided with motherboard, because they all written for Windows.
Then i heat up my soldering iron and think to hardly tie +5vsb line from PS to all ports, because i do not need 'smart' motherboard - i need *reliable* motherboard. I do not need any over-current capability of ports, i need no more than 500 mA...
...But i suddenly notice that *keyboard* PS/2 port also powerless after shutdown.
Then, using 'Power - APM configurarion - Power On by PS/2 keyboard' bios settings return power to PS/2 port, and, USB ports also now powered even after shutdown. But ... for others, suggestion like "turn on your PS/2 port to get USB work" can sounds like joke.
My board is P7H55-M/USB3. But such problems exist on other boards, like P5QL. This board *have* all needed hardware jumpers 5V <-> 5VSB. But... They are simply not work! Ports are not powered until you change something in BIOS (i do not remember exactly what settings i was use).
As a conclusion: Motherboards tend to go more smarter and consequently less useful. Get ready.
Keywords: USB, power, powering, 5V, +5V, 5VSB, +5VSB, sleep, shutdown, tweak, FET, jumper, BIOS, mA, ATX