I have experienced this, but only with some real Yahoo! users, so I’m assuming it’s down to the version of the Yahoo! client.
I run Trillian 2.012 now, the latest patch, but it’s been the same since I started on 0.74. The thing is, some people appear online just fine, some people appear offline but when I send them a message they respond and then become online, and some people appear offline and never get my message at all. Yet I know they are online because they are sitting right next to me. Very odd.