Why are the Trade Federation in league with Sidious after Dooku's lines in AOTC...

Dooku explained to Obi Wan that the Trade Federation turned to him after they were betrayed by Sidious. He continues by saying Sidious controls the Senate and is thus Palpatine. This implies he recieved the information from the TF. Why then do the other separatists such as Grievous not know this also. And why, after we are told that the war began as a result of the TF's ill-fated allegiance with Sidious, are they back serving him despite knowing the truth ? It is a very unclear subject to me.

Dooku explained to Obi Wan that the Trade Federation turned to him after they were betrayed by Sidious.

This happens over a period of time. They turned to Dooku, but they didnt know Dooku was with Sidious. Then over time, Dooku must have convinced them they needed Sids help. Remember, with the way Sids plans stuff, they had no real choice.

Two answers here.

1. Dooku was lying to Obi-wan. Nute Gunray knew that he wasn't going to hang and thus he went along with their plans for domination.

2. In "Labryinth Of Evil", Nute Gunray did feel betrayed. But as time passed, he began to suspect that Sidious was the one who was manipulating all four trials to end like they did. It wasn't until after fleeing Geonosis that Sidious revealed himself as the cheif architect of this insidious plot.

The separatists didn't know Sidious was Dooku's master until after the war had already begun, as darth-sinister said. And I think that by then it was too late to turn back. They were already too involved.

How do we know Dooku wasn't lying through his teeth when he said that? He was lying about wanting to destroy the Sith...

I think that painting Dooku as an outright liar doesn't give enough credit to his character. The way I see it is this: Dooku has sort of a dual-personality. One side is the evil Sith Lord that wants to destroy the Jedi and conquer the Republic. The other side is his more Jedi-like side.

Basically what happens is that while in his Sith Lord mode, he trains under Darth Sidious, learns the dark side of the Force, and realizes that Darth Sidious is Supreme Chancellor of the Galactic Republic. When he confronts Obi-Wan however, his Jedi side emerges, and he basically tries to slap him in the face saying, "Omg, you idiots, you're serving a corrupt Republic being lead by a SITH LORD". Then he goes into his "together we can destroy the Sith" blah blah blah because that is the very ideal that he lived by when he was a Jedi. However, when Obi-Wan refuses to join him, when the Jedi shows up with their clone army, Dooku is astounded at how "stupidly pathetic and ignorant" the Jedi are. He ultimately decides the Jedi must be destroyed and goes back to work for Darth Sidious.

Dooku was trying to get Kenobi to turn or at least plant seeds of doubt in the Jedi order.

He would use any means to do so, and lying would not be below him at this point.

I have to say that dooku was not lying about that to obiwan and in fact they were betrayed by sidious because at the very end of the phantom menace they were captured and arrested. so in retrospect sidious betrayed them by allowing them to get arrested and not help them escape. then they turned to dooku for help and by that time he was already with sidious so they probably decided to just go along with it and figured we cannot do this without him being involved somehow.

also on a small note nute gunray and the rest of the seperstist leaders pretty much did'nt want to go into a war because at the very beging of the prequels they were kinda afraid to do something to naboo but then sidious pretty much forced them to do and start them into his plans.

Nute Gunray was motivated by greed.

After Gunray realized that Darth Sidious would protect him while he amassed wealth and posessions by being in league with him, he was willing to go along with whatever the Dark Lord asked of him. Unfortunately, he did not realize he was only a pawn in the larger plan.

Which goes to prove that Nute is the one who is brain dead.

Dooku was telling Obi-Wan that Sidious betrayed the Separatists, not Nute directly. Nute is braindead. He knows things ended up not the way he would have desired. But he isn't smart enough to figure that he was tricked by Sidious. From Nute's perspective, it was because of the attack of the Jedi, not a preplanned attack all planned by Dooku and Sidious.