I actually found a solution to this problem with smart youtube.
1. Go to plugins menu i wordpress.
2. Press edit on smart youtube plugin.
3. On your right of the screen you will see the headline "plugin files"
4. Press on the file: smart-youtube/smartyoutube.class.php.
5. Press Ctrl+F on your keyboard and search for: wmode
You will find something like
<param name="wmode" value="transparent">
Delete that and replace with:
<param name="wmode" value="opaque">
6. It should look like this when you're done
<span class="youtube">
<object type="application/x-shockwave-flash" width="$width" height="$height" data="$video_url">
<param name="movie" value="$video_url" />
<param name="allowFullScreen" value="true" />
<param name="wmode" value="opaque">
</object>
7. Now, search for: embed src
You will find something like
<embed src="$video_url" type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="$width" height="$height"></embed>
Right after: x-shockwave-flash"
Add the line: wmode="opaque"
8. It should look like this when you are done
<embed src="$video_url" type="application/x-shockwave-flash" wmode="opaque" allowfullscreen="true" allowscriptaccess="always" width="$width" height="$height"></embed>
Now you're done, just press on the update file button on the bottom of your screen.
Just ask if you have any questions or if my guide doesn't work.