When Masaki was infected by White, the infection was held at bay by Isshin's spiritual power, anchoring them and thus deeming him a mere human. In the Manga, Isshin did not see Rukia when he entered Ichigo's room in the first Chapter. He had no spiritual power until the Hollow inside Ichigo took control, thus destroying the anchor that tied to two of them together. Isshin's Shinigami and spiritual powers returned to him then.