How are you viewing the logo? In Internet Explorer or another web browser?
I've found that when I export to SWF using RAVE, if I just view the SWF itself without putting into a web page (table, CSS, etc.) that it is never the correct size in appearance on the screen.
Try creating a table with a TD that is the dimensions of your GIF and place the GIF in the TD. Then view the page and see if the animation is correct.