Been tearing my hair out over one wrongly-located chunk. Was about to give up. Minecraft's output would note MC found it upon loading the map and claimed to fix it (but it would still be wrong on next load). I hadn't noticed that it was saying this once per map load until the error was in every generation of backup I still had. Each of those maps would eventually go from suck to blow, MC's fps would drop to ≈1, and it would spam my syslog with hundreds of lines per second of "Wrong location! [email protected]" and stack traces.
tl;dr: Epic. Registered just to say thanks.