One of the biggest issues we see with Sphinx Search is problems with file permissions.

If the Web server runs as a different user than the cronjobs or from the manual users who might have run cronjobs via shell, then it can create file permission issues.

Here is how we advise customers to resolve this issue:

  1. Delete the folder [magento root]/var/extendware/ewsphinx
  2. Run as the same user as the web server: php [magento root]/shell/extendware/ewsphinx/reindex_all.php
  3. For good measure run: chmod –R 0777 [magento root]/var/extendware/ewsphinx 
  4. Ensure cronjobs, webservers, and any manual running of scripts always is using the same user to avoid file permission issues