It would appear the highlighter option to enab/disab highlight common words is out of sync with smart highlighting option.
If smart highlighting is enabled under the general settings common words are always selected regardless if the highlight common words is enab/disab in the highlighter options section.
Once one disables smart highlight the highlighting of common words no longer occurs, under this condition enab/disab highlighting common words has no effect.
Please note going in and out of the options dialog numerous times eventually requires the "OK" button to be pressed multiple times to exit the dialog, while initially the operation only requires a single press of the "OK" button to exit the dialog.
Also noticed some GUI lag occurring in the Find Modal Dialog with repeated entries and exits of the options dialog, my machine is pretty stout and it is currently running a fresh OS, other than MS Office, RAD Studio, Hurricane Script Tool, and Autocad there are no other installed apps.
I think the GUI skin you have going on is awesome, the ability to toggle heights and fonts throughout is great for older eyes like mine but I think something is happening that may be worth investigating when you're bored and have absolutely nothing else to cleanup in the app

Also an import / export option function would be useful for general settings, could lead to establishing working profiles.
Best Regards
-Tim C.