I'm having the same issue where the device won't enumerate in Linux (Ubuntu 14.04) when in bootloader mode. I have no problems connecting to it when it is NOT in bootloader mode.
What I have found is that the bootloader itself seams to release the port assigned by udev (syslog):
Dec 13 22:36:09 RC-UVisor kernel: [2079069.271295] usb 3-6: new full-speed USB device number 120 using xhci_hcd
Dec 13 22:36:09 RC-UVisor kernel: [2079069.288990] usb 3-6: New USB device found, idVendor=1b4f, idProduct=0008
Dec 13 22:36:09 RC-UVisor kernel: [2079069.288993] usb 3-6: New USB device strings: Mfr=1, Product=2, SerialNumber=0
Dec 13 22:36:09 RC-UVisor kernel: [2079069.288994] usb 3-6: Product: IOIO
Dec 13 22:36:09 RC-UVisor kernel: [2079069.288995] usb 3-6: Manufacturer: IOIO Open-Source Project
Dec 13 22:36:09 RC-UVisor kernel: [2079069.289574] cdc_acm 3-6:1.0: This device cannot do calls on its own. It is not a modem.
Dec 13 22:36:09 RC-UVisor kernel: [2079069.289591] cdc_acm 3-6:1.0: ttyACM0: USB ACM device
Dec 13 22:36:09 RC-UVisor mtp-probe: checking bus 3, device 120: "/sys/devices/pci0000:00/0000:00:14.0/usb3/3-6"
Dec 13 22:36:09 RC-UVisor mtp-probe: bus: 3, device: 120 was not an MTP device
Dec 13 22:36:09 RC-UVisor ModemManager[775]: <info> (tty/ttyACM0): released by modem /sys/devices/pci0000:00/0000:00:14.0/usb3/3-6
Dec 13 22:36:09 RC-UVisor kernel: [2079069.395467] usb 3-6: USB disconnect, device number 120
It seems to keep disconnecting and reconnecting. I also had this issue in windows, but after connecting and disconnecting a coupe times I was able to get it to work.