Programmer stops responding and usb is not found after few uploads

Using Arduino Installation & Troubleshooting
#1

Hi

I'm getting a weird "programmer is not receiving error" with my UNO R2, I've looked for possible solutions but none helped. Most of them couldn't upload the sketch even once, I can upload a few times before the error occurs.

This problem started after I upgraded my computer to new Gigabyte Haswell motherboard. After a few uploads (about 3, 4 uploads) the programmer is not responding anymore. Sometimes the programmer stops responding mid upload. The only solution I've found is to reconnect the USB cable. After that it works again for a few uploads. I believe there is something happens on the OS level when "upload" is pressed since this is only happening in Ubuntu 13.10, on windows it works fine. I've followed the installation guide, is there anything else that should be set in Ubuntu?

I've tried as many different cables as I could find and all the USB ports on the motherboard, changing baud rate doesn't help, same with 1.5.5 beta IDE. Also If the upload is successful, serial monitor will work just fine. Did anybody else had a similar problem, what would be a possible solution?

After a few successful uploads, this is the error returned

avrdude: Version 5.11.1, compiled on Apr 28 2013 at 18:46:46
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/usr/share/arduino/hardware/tools/avrdude.conf"
         User configuration file is "/home/me/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : /dev/ttyACM0
         Using Programmer              : arduino
         Overriding Baud Rate          : 115200
avrdude: Send: 0 [30]   [20] 
avrdude: Send: 0 [30]   [20] 
avrdude: Send: 0 [30]   [20] 
avrdude: ser_recv(): programmer is not responding
avrdude: stk500_recv(): programmer is not responding

and with "shift+upload"

avrdude: Version 5.11.1, compiled on Apr 28 2013 at 18:46:46
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/usr/share/arduino/hardware/tools/avrdude.conf"
         User configuration file is "/home/me/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : usb
         Using Programmer              : stk500v2
avrdude: usbdev_open(): did not find any USB device "usb"

Thanks

#2

There have been reports of issues with USB/Serial converters (of various sorts) having problems with some USB3.0 ports.
If your motherboard has USB2.0 ports as well, try one of those, or perhaps insert a USB2.0 Hub in between the MB and the Arduino.

#3

I borrowed usb 2.0 hub to try it. It happens less often now, around every 10-15 uploads, so it's a bit less annoying. I'll try to see if I can find another 2.0 usb hub to try.

Thanks for the hint

#4