See http://moodle.org/mod/forum/discuss.php?d=113752

The issue seems to be

(mysql): UPDATE mdl_config SET value = '2.0071E+9' WHERE name = 'version'

Note that the version number has been rounded (value = '2.0071E+9') so the upgrade continues from the wrong place.

http://www.php.net/manual/en/language.types.float.php seems to say that PHP floats always use 15 decimal digits of precision internally, so my diagnosis is that the error occurs when the float is converted to a string somewhere in set_config before it is stored in the DB.