I see this had been dead for over a year, but it ranks first in Google for 
me. If you are reading this now, you probably didn't see the modem manager 
blacklist steps 
here 
https://github.com/ytai/ioio/wiki/Using-IOIO-With-a-PC#connecting-the-ioio-as-a-serial-port
 

The system is trying to probe this as a modem and at some point it sends a 
command that causes the IOIO bootloader to disconnect and reconnect.

On Wednesday, May 28, 2014 at 10:48:53 AM UTC-5, Ytai wrote:
>
> Thanks for the data! I'll definitely use it when it's time to fix this 
> issue. For now,it does not seem like a huge problem, as it seems to be 
> specific to a small number of Linux versions.
>
>
> On Sun, May 25, 2014 at 10:21 PM, Mark z <[email protected] <javascript:>> 
> wrote:
>
>> I just tried that test and it makes no difference, still stuck in 
>> connect/disconnect.
>>
>> I think the next thing to try is to load up a bare bones firmware that is 
>> as nearly identical to the bootloader as possible and go from there. I 
>> haven't read up on firmware coding so this problem is quickly moving out of 
>> my league.
>>
>>
>> On Tuesday, May 20, 2014 9:18:08 PM UTC-4, Ytai wrote:
>>
>>> Good idea! Let me know how that goes.
>>> On May 20, 2014 10:00 AM, "Mark z" <[email protected]> wrote:
>>>
>>>>
>>>> I was thinking if there is absolutely no difference in the code that 
>>>> establishes the handshake to the PC then maybe somehow the timing of 
>>>> manually removing the boot pin jumper by hand after connection is causing 
>>>> an issue. I'm going to try another test where I put the board into boot 
>>>> loader mode using the 5v adapter, remove the jumper and then connect the 
>>>> usb cable while the wall charger keeps the board awake.
>>>>
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>

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