If only a post's author and one comment are having a conversation then any @ notifications between them are removed from the start of comments on the grounds they are considered noise (this is presumably also why they are not in the auto-complete).
This will not happen if any other person is involved in that comment thread.
(For ref see http://meta.stackoverflow.com/a/97290/147926 and http://meta.stackoverflow.com/a/97099/147926 among probably others on MSO)
For the sake of completeness, I guess I should point to the How do comment @ replies work? FAQ post, in case you want more detailed information in general.
As a side note, comments that attempt to ping multiple users (ie, multiple @'s) are also blocked, the work around (a backtick) will cause only the first @ to be notified.