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Try sleep(.1) between rednet messages. Maybe server lag? Also, a good habit to get into, especially when using startup is to shell.run("id") in the beginning of the startup file. This way the turtle will print to its terminal and identify itself.
Best way I found to attack and empty inventory is this. This assumes the chest is below the turtle.
while true do
turtle.attack()
for i=1,16 do
if turtle.getItemCount(i) > 0
turtle.select(i)
turtle.dropDown()
end
end
sleep(1)
end
Assuming it even works. Capacitors recharge pretty slowly and clusters add flux to your world anyway. So again, what would be the point? You'd still be adding flux to your world. You're better off just breeding some bees to purify the nodes. Although a crazy turtle through teleport rotation...
In the launcher go to Options->Advanced Options. Try putting -XX:MaxPermSize=128M into the additional java settings option. This worked for me on my laptop.