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"The Connection was reset" in iframe

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The same server is being used for the main html page (generated by a server-side Perl script) and the content within an iframe (a call to another Perl script on the same server). I have a perl script being called in my iframe. The script works fine, I've tried it on it's own within the browser and it works within the iframe EXCEPT when the script calls a query on a MySQL database that is rather lengthy. In my case I search my records that have IDs containing "11" (returns like 1,000 records) and it works fine. If I search for "1" only it should return like 5,000+ but instead I get a "The Connection was reset" message and that sad face icon. It does not take the error message long to come back, within 2 seconds so I'm left wondering what is causing this to happen and how I can fix the issue? If I redirect the output from the Perl script on the server to a file the content is completely sent there -  ruling out an issue with the script or aborting because of number of records or something.
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