I've been using cygwin for a year now, and I have no problem executing code from any directory. Are you putting a "./" infront of your executable and are you compiling it with gcc? Also, is it a real executable or is it object/byte-compiled code. Sorry for the stupid questions, but sometimes people make foolish mistakes (Like wondering why a filesystem wouldn't show up...turns out in my 3 am daze, I forgot to __make__ the filesystem...oops)
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