With regex's you need to accommodate for white-spaces and the like. In Fortinet configs there are frequently white-space before the actual command happens. Using '^' anchors the regex to the beginning of the line.
So, what you probably really want to use for something like that is "^\s*set pre-login-banner enable" to allow for as many white-space characters before the actual "set" command happens. If you want the line to terminate after "enable", add a "$" at the end to make sure the line ends there.
A nice and easy way to see if your reg-ex's work is to edit the file using the GVIM editor in windows. Put in a "/" to search followed by your regex, it will highlight occurrences in yellow that match.