Running CiviCRM 4.3.8 on Drupal 7.37 (for now, but we're in the long process of a major upgrade of our website). Often I have to update the paths because they revert to a different docroot which may have been originally set up for testing purposes. (Let's call them A and B, A is the correct one and B is the wrong docroot.)
When it reverts seems to be at random and I cannot find the cause, but it causes problems such as emails going out with links to a test website in B's docroot, the reports will not load, etc.
Update file paths settings will show:
Old Base Directory - /var/www/html/B/docroot/sites/default/files/
New Base Directory - /var/www/html/A/docroot/sites/default/files/
Edit: The CiviCRM installation is in a separate docroot from the Drupal installation (for now) and uses symlinks in sites/all/modules in order for Drupal to find it.