Finger in the air guess here, but are you manipulating an output file's name, and if so could the regexes have been subtly broken and accidentally set the name of the output file to be the same as the script?

In short, 'Is this your output file'?

Yes, I appreciate this would involve quite a few nasty configuration mistakes.. especially with permissions in the cgi-bin directory, but I know I managed to do this kind of mistake in my first job.