The default functionality in PHP 5.4 is having no Safe Mode at all.
That is similar to the past when the Safe Mode directive was set to off.
Whatever is causing your problems, it can not be Safe Mode in PHP 5.4 because there is no Safe Mode any longer. It has been removed.
If you want to find out what causes you headaches, you need to troubleshoot your problem. For example by enabling error logging and reporting to the highest level and following the error log.
See as well: