Annoying PHP - MySQL communication timeout

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Has anyone here experienced a problem where a MySQL server seemingly
closes a connection opened by PHP whilst the PHP script is still
running?  The problem only seems to affect scripts that run for a long
time but there are a few things that make it unusual:

1) There is no obvious correlation between the time taken for this to
happen and any of the MySQL timeout variables
2) MySQL logs nothing in its error log i.e. no "connection aborted" or
similar
3) PHP hangs indefinitely as if waiting for a response (a blocking read
according to strace) and there is no "MySQL server has gone away" or similar
4) This is not one of the numerous MySQL bugs that can be triggered
repeatedly by sending a particular SQL query
5) Calling mysql_ping() before each query attempt gives no improvement

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