I had the same problem and had a hard time solving it, but I found a solution!
I read an article that says that if thumbnail width >= header width then it uses the thumbnail as a header replacement.
If you are using the functionality the same way as I do, you don't want the thumbnail to be that big anyway so what you may have to do (espacially if your theme is based on twenty ten) is :
1. open functions.php
2. find this line : set_post_thumbnail_size( HEADER_IMAGE_WIDTH, HEADER_IMAGE_HEIGHT, true );
3. Make it a comment using /* */
4. Add a line under this line that looks like this : set_post_thumbnail_size( width, height, true/false );
Hope this will help you!