I've experienced the same problem.  My BBB does not recognize newly plugged 
in USB hardware (an XBee dongle and an Arduino).  I'm running Debian with 
kernel 3.8.13.  I can "wake up" the USB by typing:

lsusb -v

After issuing this command, my USB device powers on and runs as expected. 
 The -v is important.  Without it, the hardware remains powered off and 
unrecognized.

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