Steps to reproduce:
1. Build any project as WP8 visual studio project
2. Open its WMAppManifest.xml. Under Tokens element add the following line:
<Extensions>
<Protocol Name="angrybots" NavUriFragment="encodedLaunchUri=%s" TaskID="_default" />
</Extensions>

3. Build and deploy it to device
4. Using device, browse to a page which has the following link:
<a href="angrybots:">Launch Angry Bots!</a>
5. Click on the link
6. Built application will launch but will immediately exit after a splash screen.

More information regarding URI associations: http://msdn.microsoft.com/en-us/library/windowsphone/develop/jj206987(v=vs.105).aspx

Why is it not going to be fixed?
If handler is added to the Manifest, it also has to be implemented in code. Microsoft documentation specifically says that.

In this case, UriRemapper has to be added.

Define this class:

class UriRemapper : UriMapperBase
{
private readonly Uri _mainPageUri = new Uri("/MainPage.xaml", UriKind.Relative);

public override Uri MapUri(Uri uri)
{
var uriString = HttpUtility.UrlDecode(uri.ToString());

if (uriString.Contains("angrybots"))
{
return _mainPageUri;
}
else
{
return uri;
}
}
}

And then add this line to InitializePhoneApplication():

RootFrame.UriMapper = new UriRemapper();