Board Thread:Questions and Answers/@comment-6207546-20130504124857/@comment-893506-20130505035533

Mubixx wrote: All captains are known by EVERYONE in the Gotei 13, even the lowest class officers so its impossible that a seated officer like Rukia wouldn't

Rukia was never a seated officer. She had the abilities of a seated officer, but she was never a seated officer, since Byakuya's influence initially denied her a promotion. She was only a lieutenant, and that was after the 17 month timeskip that occurs during the story.

Anyway, Isshin's appearance did change since he was a captain 20 years ago, so it's not entirely unbelievable to think that Rukia didn't know Isshin Kurosaki was actually Isshin Shiba.

In any event, it's all speculation, as Tite Kubo did not seem to consider it an issue in story, so he didn't elaborate on Rukia's failure to recognize Isshin in the manga.