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At the beginning of the series after Inuyasha is freed from the Goshinboku his memories and his feelings for Kikyō are still very fresh in his mind, and when she is resurrected Inuyasha is shocked to see her and his feelings for her come rushing back. Because, in Inuyasha's mind, it was only a few days ago that he saw her and was in love with her, even though fifty years had passed. Additionally, in the early parts of the series Kagome and Inuyasha have not yet formed the bond that they do as the series continues.

The short answer is that at the start of the series Inuyasha was still very much in love with Kikyō and had not yet bonded with Kagome to that extent.