Apache server returns 404 after timeout

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http://serverfault.com – Making multiple requests to the server causes a 404 error after about 40-60 seconds. I am using JavaScript to request: example.com/test/location. Apache has mod_rewrite enabled that maps this to the file index.php. index.php waits for 10 seconds before returning 200. The JavaScript immediately requests again on return. Watching the Apache access.log I can see: index.php 200 index.php 200 index.php 200 index.php 200 index.php 404 This makes no sense to me as the index.php file has not moved. Any ideas what is going on? Unfortunately this is hosting with CPanel so debugging is limited. (HowTos)