Yes, you want to have IPB manage making links https instead of using htaccess or something similar to redirect. Chrome does not see the redirect until the response and as a result, it can complain when the button or link is clicked initially.
Basically make sure SSL is installed/configured for the domain on the server and then modify the conf_global.php and everything should be good! Clearing the system cache just makes sure any system links get updated quickly so those http links get fixed sooner. 🙂
