Wait a minute, are we talking about Flash? the Macromedia software for animated things? this is a client component, ispconfig has no relation with what you put inside your pages !
Look for errors on other places, check if your .swf file is uploaded in the place when it should be, put the .swf address right into your explorer, did it open? is there any security setting in your computer? IE ussualy block any "insecure component", this is NOT a server issue.