Technically the calibration is not complete until all LEDs return to normal state. At least that's the way I read the code.
Hi Glenn, are you sure the calibration is completing correctly? Are you watching the communications console by any chance? It might be giving an out-of-memory error. Unfortunately there's no other indication of this except by watching the messages. If you got the r386 build from the AQ FTP site experimental folder, then that could very well be the issue (some of those builds have actually been pulled).
-Max