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I just checked the mac mini again and now the external drive is an option. I was literally about 99% sure that I was booted from the internal drive. In fact, I seem to remember going in to /volumes to check as well. If it happens again, I'll do some extra checking and let you know if I find anything.
The weird thing is that I have used sd on my mb pro with no problems at all. Oh well,this is one of those times when I hope it is human error on my part, but am not sure that it is.
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