Is it possible to power up ports on a USB hub from Ubuntu?
hub-ctrl will do what you need.
sudo apt-get install libusb-dev
cc -o hub-ctrl hub-ctrl.c -l usb
sudo ./hub-ctrl -v
sudo ./hub-ctrl -P 2 -p 1 # turn on port 2
sudo ./hub-ctrl -P 2 -p 0 # turn off port 2
Disclaimer: although I have tested it on Ubuntu 12.04 (precise), I did not write this utility. It does require a hub with built in power control, but given that your hub is powering down certain ports it is a good bet your hub has it.