Yun sketch not working on reboot

When I power off the Arduino Yun, next time it powers on, the 32u4 sketch doesn’t work. I must press the 32u4-RST button on the board, to get it to work again?.. Is there a fix for this? Maybe a way to reset the processor through the linux side?

http://forum.arduino.cc/index.php?topic=240239.msg1804522#msg1804522