Sometimes it happens like this, when we are not able to upload any *.swf file using the Media Manager option but simultaneously it works fine for file of any other extension.
Solution
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Go to Site – > Global Configuration-> System
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Now make sure that .swf option is included in the Legal Extensions (File Types) and Legal MIME Types. If not add .swf option to both the text boxes.
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Test uploading. Problem Solved.
 
