Checked all permissions. The apache configuration has apache as the user that executes and the file is 666 and owned by apache when it is finished. The parent and its parent are 777 (also owned by apache). Error logs are empty of any references to this. That's why I don't get it. I'll try the perl chmod suggestion to see if I get error reporting and let you know.
I am presuming that the configured user for apache (called apache) is what is running the script.