One in the description of the image in the tag in the Header section of the skin. (I assume this is header.vm.)

<img src="$logourl" alt="XWiki" width="440" height="108" />

The second place is in the style section where the banner size is defined. The height should be equal to the height of the image.

#xwikibanner {
 height: 110px;
}

PS: thanks for the contribution Carolyn