I'm having problems trying to duplicate this bug so that I can work on fixing it.  Could you please tell me what steps you're following to make this bug pop-up?

This is what I've tried: (small update)

1. Start with a demo server/dev site.
   
2. Enable Meta Data on the site.
3. Go into content profiling and add a meta data tag.
4. Add meta data to an article on the front page.
5. Commit the change to the Article
6. Edit the Article template to add the metadata tag
7. I see 1 and only 1 meta tag, and it's not in the head section.

It would also help to know what browser you're using.

Thanks...

Not sure if this is related or not, but I noticed this with 7.3.8 yesterday, so I decided to upgrade to 7.3.12 to see if it would fix it, but it's still showing up.  If I have an Article Asset and enter information into the header portion.  For instance, here's the content of text box for the extra head tags: 

<style type="text/css">
        .timeLabel {
            float: left;
        }
</style>

 Here's how it's showing up in page source when it's rendered (including the top/bottom boundary lines for reference):

<script src="/extras/contextMenu/contextMenu.js" type="text/javascript"></script>
<style type="text/css">
        .timeLabel {
            float: left;
        }
</style>
<style type="text/css">
        .timeLabel {
            float: left;
        }
</style>

<script src="/extras/draggable.js" type="text/javascript"></script>

That helped a ton.

I wasn't testing with the Raw Head Tags, but with actual Meta Data from the Content profiling section.

I was able to confirm your bug and fix it.  The fix will be available in 7.3.14.