The issue you describe sounds pretty weird, in my personal experience I've never faced such issue. So, right now the only suggestion I can think of is to try to reflash your board to see if that helps.
Seems like it is related to the latest release ww25.5-15, I downgraded to ww18-15 and it solved the problem. So I decided to upgrade again to 25.5-15 but the problem appeared again, so i'll just stick with the previous firmware.
Thanks for your advice.
Here is how I managed to fix this issue or at least work around it.
1st create a startsketch script under /sketch:
# script to start arduino based sketches
if [ -f $1 ]
echo "file $1 exists"
echo "preparing $1 with chmod"
chmod +x $1
echo "starting $1 as background process"
./$1 /dev/ttyS0 > /dev/null 2>&1 &
echo "file $1 does not exist"
Then make it executable
chmod +x startsketch
it should start your sketch
next cd /etc
then make it executable
chmod +x sketch.sh
Now test it:
it should start sketch.elf
Make the script run at every boot
Now reboot and voila latest firmware and auto start sketches
The real issue is why should any user have to go through what you did?