Ush, you are generally bright, but in this case, you are overlooking CANON in the movies themselves.
When Qui-gon encountered darth Maul in TPM, did he tell the jedi council, "i think he was someone who used the dark side of the force?" NO. he said, "i think he was trained in the sith arts" or something to that effect. That perked up everyones interest because of the appearance of the sith possibly had some relationship to the prophecy regarding the chosen on. further, kai adi mundi wanted obiwan and quigon to draw out their attacker, so, as mace windu put it, they could "unravel the mystery of the sith."
Further, the jedi knew there was a sith master and an apprentice, they knew obiwan killed one of them on naboo. Yoda said there are ALWAYS TWO. NO MORE and NO LESS. so at the outset of AOTC, they know there are still TWO sith.
While the jedi beleived Dooku to still be good at the beginning of the movie, they realized his true nature by the end of the movie. Obiwans expression when dooku was interrogating him, and asking for his help in crushing the sith clearly point out two things.
1. that The jedi STILL belevie the Sith are a powerful force behind what is going on.
2. Obiwan suspects Dooku MAY be sith.
Further, the outcome of the battle with Dooku and the fact that the dark side is growing clearly give evidence the jedi feel Dooku is one of these two sith, since they witnessed him in action.