Hey,
I've been in the process of making a world, but nearly every time I change any of the settings in the config files and restart the game after deleting regions, the world just has no ores or stuff like gravel in it? I've tried determining which specific settings cause this, but it seems to be random - most times it happens, a few times it doesn't. This is both happening on Singleplayer and on a server.

I have noticed the same problem. Most likely what you have done is you leave your biome config files open when you generate, no? You can't see what's been changing, then. What's going on is your source blocks and block types that have block data as :0, for instance, GRASS:0 or STONE:0, or simply GRASS or STONE are having extra ":0"s written out to them every so often time you change something about them. So if you start out with block type GRASS and change the config TC will annoyingly and automatically write it out to GRASS:0, and the next time you change it TC will write it out to GRASS:0:0, which is obviously invalid. Most likely, the only reason it does not write it out to GRASS:0:0:0 is because it already detects an error and ignores the text altogether.

The only solution is to either reload the text file when it happens and manually remove all the errors, or else keep the config open with the correct syntax, save the document twice before generating so the current text overwrites what it was trying to change it to (like it never happened) and go on your merry way.

If this is the same error, you should notice replace blocks and surface control work just fine when ores and things don't (as long as they don't rely on an ore you generate). Hopefully this annoying as hell bug can be fixed soon....