Check the 5keys.html file with TextWrangler. IIRC, KindleGen only accepts UTF-8 and Windows-1252 (and the new versions prefer UTF-8). The text encoding applies to the entire file, not just any one line.
In any case, since you've said that your TOC, NCX, and start points are all ignored, very likely something has gone wrong in your <guide> and/or <manifest> section as previously suggested.
Possibly Amazon has updated how they want things to be referenced in the OPF, and you may want to check against the latest version of the
Kindle Publishing Guidelines to make sure your files are specified in the way that the latest KindleGen/Previewer want, if anything's changed since the older versions.