Board Thread:Questions and Answers/@comment-1754938-20150922055002/@comment-26269901-20150922073556

Rukia most likely never met or seen Isshin in the past, given that they were different squads, and during her stay in the Kurosaki house Isshin was still without powers and essentially a human like any other. People speculate Isshin later on simply avoided contact and hid his presence. No one would really expect the vanished former captain to be residing there, so it shouldn't have been that hard.

Though I gather Kyoraku, being far more observant and experienced, would have noticed something, hence why I'm sad his visit to the Kurasakis was merely mentioned briefly, but never shown.