Yus

But, that’s the only thing that changed in version 3.1.3. If you did what I said above, you’re back to the previous version (3.1), so if it worked fine with your theme before it should also work now.

And I just checked in IE9, both versions work (with the default theme), try clearing your browser cache and check again.

Sorry about that, open at-reply.php and replace
.comment:hover .yarr { visibility:visible }
with
li:hover .yarr { visibility:visible }

You don’t have to do this if you’re using the latest version of the plugin (3.0.5).

Otherwise, it’s in at-reply.php.

This should be fixed in the newest version, if you want to do it manually, just replace:
add_filter('get_comment_text', 'yus_reply_arr');
with:
add_filter('comment_text', 'yus_reply_arr');

Thanks for letting me know. ??

Yes, you can also remove that if statement.
I tried using a TinyMCE focus function but I don’t know why it also fails. :\

Anyway, this should do it :

function yus_replyTo(commentID, author) {
var inReplyTo = '@<a href="' + commentID + '">' + author + '<\/a>: ';
insertHTML('<span>'+inReplyTo+'</span>');
location='#comment_parent';
}

It’s a bit dirtier than focus() but at least it works.

Try with myField.focus(); just after insertHTML('<span>'+inReplyTo+'</span>');

MCEComments provides an easy fix on the page you linked. It’s for WP Grins but also works with @ Reply.

Edit the at-reply.php file, search for:
myField = document.getElementById('comment');
and replace it with:

myField = document.getElementById('comment');
insertHTML('<span>'+inReplyTo+'</span>');
return;

And… it works. ??
You can also remove everything that follows (because it’s not needed anymore), up to :

}
}
	//]]>
</script>

which you must leave that way.

I hate plugins that break your WordPress installation too, that’s why @ Reply doesn’t change anything to your files or database, it just adds some JavaScript/CSS and when it’s disabled and/or deleted there’s nothing left from the plugin.

Let’s start from the begining…
1, 2) OK.
3) You have a custom theme, you need to customize the CSS so that it’s not off positioned. You may also need to customize the JavaScript if your theme’s HTML is really different from the default WordPress theme.
4, 5) OK. Now it should be like you never installed the plugin.
6) There’s no way this is caused by “@ Reply” if it’s disabled and/or uninstalled. Maybe you’re seeing the cached version from your browser and/or a cache plugin.
7) You don’t need to reupload anything, no files were changed by @ Reply.
8) That’s because the plugin doesn’t touch to your files.
9, 10) I don’t know, am I supposed to guess your URL and/or theme code? Did you clear your browser cache? Are you using a caching plugin?

My suggestion would be: let me know where I can see your theme, and what plugins (especially cache plugins) were running on your installation. Then maybe I could stop guessing and start solving your problem.

Oops, didn’t see this topic. ^^
I just uploaded a new version which supports paged comments.
It should be available in a few minutes. ??

Edit: it’s available. ??

Someone asked me for this a few months ago, here’s the code change I suggested :
<a href="#" title="Reply to this comment" onclick='yus_replyTo("<?php comment_ID() ?>", "<?php comment_author();?>");return false;'>Reply</a>

Maybe I should add it to the FAQs ?