So here's a report from user Cr9 who managed to poke around the graphics problems:
The first time you start the game with graphics in, they don't work. You generate a world, or go into arena; nothing works. Puzzled, you back out and do something else -- but zounds! The Es and Ds and Hs and numbers have vanished! Some walls too! You exit the game after your world generated, and come back later, and boot up DF mode, and what? The graphics work! Arena still won't, though.
So here's my interpretation of it: The first time you load the game, the graphics load for DF and AD mode only (?!) though it doesn't matter because you have to generate a world before you can see that. The graphics never load in Arena mode for some reason without messing up the tileset.
When you generate a world, the graphics break the tileset for some reason. That also happens if you enter Arena two times in a row. If you exit the game, and come back in to use the generated world, NOW graphics have loaded and unless you gen a new world or go into Arena, the graphics and tileset will stay loaded and work.
When trying to enable a graphics set in the usual way, the result is the default example graphics from Toady (The normal dwarf, a miner and a dwarf with an "M"). This happens even if the example graphics file is deleted from the raw/graphics folder (and it's not in the save/region1 raws either).
I suppose it might help to try and use a different set for testing this bug.