PHP and MySQL timezones mismatch over API but not in UI

CRM_Utils_System_Base::setMySQLTimeZone is the method that pulls in the CMS's timezone to correct for differences in PHP/MySQL time zones. And that method is called by civicrm_initialize();.

However, that method is NOT called when you make an API call to System.check. So you end up in a situation where a remote monitor tool (like CiviMonitor, or https://github.com/PalanteJon/check_civicrm) reports a timezone mismatch that the Web UI doesn't.

The solution is to call CRM_Utils_System_Base::setMySQLTimeZone when doing the timezone check. I have a PR for this which I'll submit once it's passed more internal QA.

Herb, this may also fix your problem in CRM-15656.