After setting font size to 75% (AKA 72dpi AKA "tiny dots") resetting, setting settings to default, setting font size to normal restarting and reloading my previous settings, I can see the configuration window... That goes to number 7 on my "strangest bug fixes" list...
Thanks for the help guys, and thanks to the devs that made this program. Time to go beat Zelda again...and again...and again...