Which is odd because the Jedi seemed in denial that Dooku would even murder someone in AOTC much less be a Sith Lord. It also is interesting that the Jedi were either slow in their pursuit of leads on the other Sith Lord after Maul's death, or Palpatine had been leading them on dead ends for the last ten years.
I don't know what the canon explanation is, but the non-canon Legends books did comment that the Jedi Council was denying what Dooku had become because they didn't want to believe he had fallen so far.
(Incidentally, the Clone Wars: Lost Missions episodes establish that Dooku was working with Sidious before The Phantom Menace happened.)