Hi David,
It sounds like your web hosting provider enforces a very low timeout for any PHP operations. I can see in your log file that PHP's "safe mode" is on:> safe_mode: 1
This feature is somewhat misnamed; the PHP developers removed it a couple of years ago when they realised that it did not achieve its aims - http://www.php.net/manual/en/features.safe-mode.php. However, one of its effects is to allow PHP to run for only a few seconds. This is sufficient to write out your entire site contents and database only on very tiny websites. You will need to turn it off to have a usable web hosting environment.
David
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