Your dots are in a different div and the flash swf is in a different div altogether. Depending on Flash export settings, the positioning will change to maintain aspect ratio of your SWF content.
One solution for you is to add the filmreel dot pattern to your Flash SWF file itself to top and bottom area and get rid of <div class="dots"></div> altogether so the dots will actually load within the SWF file itself.
On a sidenote, most modern handheld devices do not support Flash/ play SWF content. Have you considered using Adobe Edge Animate to achieve simple animations? http://html.adobe.com/edge/animate/