I have exactly the same problem.
If I disable SEF in Joomla everything works OK. With it on it dies.
.htaccess is configured correctly and all components work with SEF ON except JSMF ?
The .htaccess is modified for a phpsuexec environment and I have php.ini files in all sub directories.
There is a problem running this code in CGI somewhere.
attached .htaccess and confirmed that all files are patched
