<p>If only a post's author and one comment are having a conversation then any <code>@</code> notifications between them are removed from the start of comments on the grounds they are considered noise because post owners are <em>always</em> notified of comments whether you <code>@</code> them or not.</p>

<p>This will not happen if any other person is involved in that comment thread.</p>

<p><em>(For ref see <a href="http://meta.stackexchange.com/a/97290/147926">http://meta.stackexchange.com/a/97290/147926</a> and <a href="http://meta.stackexchange.com/a/97099/147926">http://meta.stackexchange.com/a/97099/147926</a> among probably others on MSO)</em></p>

<p>For the sake of completeness, I guess I should point to the <a href="http://meta.stackexchange.com/questions/43019/how-do-comment-replies-work"><strong>How do comment @ replies work?</strong></a> FAQ post, in case you want more detailed information in general.</p>

<hr>

<p>As a side note, comments that attempt to ping multiple users (ie, multiple <code>@</code>'s) <a href="http://meta.math.stackexchange.com/questions/2094/should-we-discourage-the-use-of-multiple-redundant-username-pings-in-comments/2615#2615">are also blocked</a>, the work around (backticks) will cause only the first <code>@</code> to be notified.</p>