I have seen this issue a couple of times, and saw a report of it on the bug tracker, and never was able to fix it without just wiping my game installation and painstakingly reconstructing it, but I've finally figured it out. So I thought I'd share it with everyone else, since it didn't seem to be recognized in the bug report, which was closed for inability to reproduce. ("Various Oddities":
http://www.bay12games.com/dwarves/mantisbt/view.php?id=2022 .)
The issue is this:
After a worldgen, you look at any spot, and, instead of the usual different types of stone and soil layers, *all* layers show as "Rock". Eight layers of it. No other info. If you actually embark, the game will either crash (as it did for me), or you'll see all sorts of weird stuff, as the reporter of the linked bug report saw.
I'm not sure if I ran across the only thing that can cause this, but I finally figured out what it was at least in my own situation. (And it wasn't anything to do with the index file.)
The problem was that I kept backup/original copies of raw files I'd modified in the raw/objects directory, and that the game was reading the entries in them as hundreds of duplicates, despite the fact that the filenames were changed (even .txt extensions removed).
Originally, I had the unchanged originals named such things as "inorganic_stone_layer (Original).txt". I then removed the extension from the filenames of all such files (names then being "inorganic_stone_layer (Original)" with no standard three-letter extension), ran a quick worldgen again, and the problem recurred. When I removed all these files from the raw/objects directory, my worldgens proceeded properly, and I again saw proper stone and soil layers. When I put them back in, the worldgen would again be borked.
One big telltale sight was an errorlog.txt filled with megabytes of entries like "Duplicate Object: inorganic LOAM" and "Duplicate Object: material_template FAT_TEMPLATE" and so on, for all substances.
Anyway, if you are seeing this error, it is easy to fix. Just delete or move somewhere else all extra files you may have put in the raws. If you have alternate copies of any of the raw files, no matter what you named them, they may be causing it.