Since I'm not having the same problem as you, even though I'm running the same version of Safari, it follows that your setup must be different from mine in some way. The most common cause of software problems is third-party system modifications. By booting in safe mode, you eliminate those. If the problem is not reproducible in safe mode, that means it's caused by the modifications (to oversimplify slightly.) If the problem is reproducible in safe mode, then it's caused by something else, such as your Safari data, or less likely, a corrupt OS installation.
There is a "reload page" action, but no "reload all pages" action that I know of. Pages sometimes refresh themselves automatically, an annoying Javascript feature, but if you have multiple sites open they probably wouldn't all do it, and certainly not all at the same time.