The chapter which reveals Kabuto's a spy and the chapter after that make no inclination as to who he served first.
It was stated that he avoided being noticed because he had always dropped out before people took notice of who attended. Sure, a few may have recognized him from exams earlier, but maybe they just thought he was a shitty ninja but didn't want to give up. He never caused any trouble before hand after all. He was just a bit more bold during these exams because of Sasuke.all this goes against the chuunin exam too, where no one knew of kabutos existence, and found it strange that some one has failed the exam 20 (or maybe it was 10) times. Kakashi picked up on it, and confronted him in the hospital where sasuke was recovering.
The only thing I found out of place with this whole thing, but it hasn't been fully explained yet, is how Danzo lost track of him.
According to this he was a Konoha black ops anbu spy and did missions for Konoha. Also most likely how Orochimaru came to know of him. His "Mother" and no one else seemed to not remember who he was and at the time I assumed it was because Danzo used his sharingan hax to make them forget stuff but maybe it was somebody else because then how would have Danzo forgotten about Kabuto?
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