I was setting up my favorite font by adding the font entries to the init file;
[FULLFONT:Metalls_Zilk_16x16.png]
[BASIC_FONT:Metalls_Zilk_16x16.png]```
but the interface width and height needs some tweaking to work with it. Upon changing the options in the game menu and restarting for them to take effect, the added entries are removed entirely.
I would wager a guess that this is because everything in the menu is saved at once, rather than just the changed entries, which probably shouldn't be like that.