Hi
I have seen Makerbot be hit or miss on shipping with the boot straploader loaded onto the chip. Since they are a startup company it's totally understandable.
The other thing is it's kind of a timming problem to get the boot strap loader to work correctly. My laptop used to be real reliable now it is extreamly hit or miss, I have to watch the disk activity light and when it starts to slow down on the compile I mash the reset button.
To tell if you have the boot strap loader on your processor, reset it. It should slow blink a couple of times followed by some rapid blinks. If it is actually loading then you get a whole series of rapid dim blinks.
If you do not have the boot strap loader on your chip you can use your TTL cable to program it. Instructions are in the link below:
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exmrclean.blogspot.com]