In the PHP 5.3.13 CLI version, it might use the "MAGIC" environnement variable to get the magic database file. Due to the fact that this version doesn't use the standard format, this file may be wrong. You can see it via a simple script :
Unset this variable and it will work again. You can use unsetenv (C-Shell) or unset (Bourne Shell).
This does not affect the Apache version. Other CLI versions might be affected.
I lost a lot of time on this undocumented issue.