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There's your problem. You didn't quote properly. Try: $ echo [:upper:] [:lower:] to see what you were really invoking, then try: $ tr '[:upper:]' '[:lower:]' to do what you meant.
My guess is that you have a file in your home directory that uses a single letter, so the bracket expansion of bash took effect and expanded to that filename rather than passing through the regex that you thought you typed.
By the way, none of this is cygwin specific.
Thanks -logu
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