I use TextWrangler and I have no problems.
Sometimes KindleGen can be picky over the stupidest things. Do you have the text encoding set to UTF-8 with Unix LF endings (and also have "use typographer's quotes" turned off)?
Alternatively, your files don't happen to be in a folder path that includes an # character anywhere in the path name, does it? I've found that KindleGen will completely ignore my NCX and other stuff without giving a warning if I have my files in something like, say "Blahblah series/#1 FirstBook" before compiling.
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