There have been several reports of Linux related problems with the IOIO in bootloader mode. You're using an unstable release, which makes it even more of a suspect. Unless you want to spend time digging deep into the system internals to figure out what's broken, I'd simply use a different OS for the upgrade process.
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Ytai,
I have also tried it on Windows 8 32 bit. Before driver installation, in Device Manager, when the IOIO-OTG was connected in boot loader mode, it appeared as IOIO in Other Devices, with a warning sign on it. It said there is no driver installed.
I forced non digitally signed driver installation, and installed the driver through Add Hardware. Another device under COM and LPT appeared named IOIO-OTG and it took COM4 port, still there was a warning sign on it. Ioiodude cannot retrieve the versions over COM4.
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