I found your replies in Adobe Forum (http://forums.adobe.com/message/4083435) and facing similar kind of issue
like application throwing "License not present. With the trial version only limited replays are allowed." Error message
when running my application for Automation compiled using SDK 3.6
Please reply back with your emai id, so that i can share the license.properties file found in “C:\ProgramData\Adobe\Flex”
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