I noticed the issue with folders, should have fixed in latest release:
OS X:
https://dl.dropbox.com/u/16806101/Ki...er_osx_2.4.zip
Win64:
https://dl.dropbox.com/u/16806101/Ki...-amd64_2.4.zip
Also, the "file not found" errors could mean that KCC cannot launch
unrar and
kindlegen, are you sure you placed them under
/usr/local/bin ?
Conversion being successful you should find a new
.epub and
.mobi files alongside the source ones!