Drush bootstrap level can cause cache problems

I have had a problem where certain things on the site weren't working properly, hook_forms wasn't calling all of the functions for example. I turned out that a module was calling variable_set() and this was causing parts of the bootstrap cache to get rebuilt inside the default drush bootstrap environment. As a consequence there were several items in the module_implements cache that were disappearing. After about a month of tearing my hair out I figured out what was happening. I added the bootstrap key to the elysia_cron.drush.inc file and it seems to have fixed the problem.

  $items['elysia-cron'] = array(
    'description' => "Run all cron hooks in all active modules for specified site using elysia cron system. Use this instead of \"core-cron\" if elysia_cron module is installed",
    'callback'    => 'drush_elysia_cron_run_wrapper',
    'arguments' => array(),
    'bootstrap' => DRUSH_BOOTSTRAP_DRUPAL_FULL,
  );