When using non-current builds placed in custom directories, the world files fail to save and load correctly.
Once a world is created, the pause menu does not display the "Saving world" message and exiting the world back to the menu is instantaneous.
Upon re-entering the world list, the newly generated world is not there.
Checking the directories, I discovered that the worlds' folders and files were all present and in order, even at the same time as the client insisted that there was nothing there.
I also discovered that for some reason the worlds existed in TWO places at once. One saves folder, in the version's directory, contains the proper files. The other saves folder, in the ".minecraft" directory, contains only a level.dat, session.lock and empty data folder for each world.
I have no idea what could be causing this.