One possible explanation may be that the PHP garbage collector interferes with the script. That is why you see random deaths. When the garbage collector is enabled, the loop search algorithm is executed whenever the root buffer is fully operational.
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[START 2011/01/21 13:12:23] MySQL Connection: TRUE [END 2011/01/21 13:12:28] Query took 5s
[START 2011/01/21 13:12:28] MySQL Connection: TRUE [END 2011/01/21 13:12:37] Query took 9s
[START 2011/01/21 13:12:39] MySQL Connection: TRUE [END 2011/01/21 13:12:51] Query took 12s