Generally, pixelation occurs when the image is at a low resolution. It may be because the image is being stretched larger than it really is. Is the resolution at 300 dpi or 72 dpi? 72 is what we use for the web, but if your logo is small, or going to be used other places, like in print, 300 dpi is recommended.
Could you post a link? I could be of more assistance if I could see it on a webpage, or online at all.
Sam