copy everything, delete the files, rerun script. Are they still being written in wrong order?
prints the system time. That should at least solve the mystery of what of written and when. 
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Most languages buffer I/O for performance, which can mean things happen when you don't expect them.
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the point is to understand what's going on. I stand by understanding how buffer works.
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it seems default Matlab is to flush buffer after each file read/write call anyway. http://blogs.mathworks.com/loren/2006/04/19/high-performance-file-io/ …
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Oh lord, do The Mathworks have to do *everything* differently?
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differently = wrongly *hides*
End of conversation
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print something like "about to write file x and time is y" where x = txt/mat & y = sys time
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also eventually in like a few months when you can move to python


End of conversation
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