Kane_Starkiller
this party's over!
Well, I'm led to believe that the time period between episodes 2 and 3 is about 3 years (not confirmed I don't think) as this is roughly the time period of 'The Clone Wars', which culminates at the begining of film 3.
With regards to the JC knowing 'what he did' I pressume you mean either:
a) the hate-filled slaughter of the tuskens on tatooine (can't think of anything else that might get him expelled)
or
b) his marriage to amidala, which is forbidden in the Jedi Code.
In both cases, I don't suppose there's any reason why the JC would even know about them. The only person told about Anakin's delve into 'the dark side' was padme, who sympathised with him as she recognised his slaughter as a means of venting his anger towards the tuskens for causing the loss of his mother, and like their marrigae (which was witnessed only by 3po and r2) is probably kept a secret by the two lovers. Who knows why Anakin is booted from the Jedi order? He and Padme have decided to undertake a forbidden relationship - perhaps by the end of the clone wars, the secrecy of their love is becoming too difficult? Maybe Anakin does something very dangerous at the end of the clone wars that endagers the life of other Jedi, in an attempt to rescue or save Padme - thus causing him to admit to them that she is his wife in order to justify his actions. Maybe his expletion has nothing to do with his marriage to Padme at all?
My guess is that once the Clone Wars have finished, he is expelled for keeping his marriage to Padme a secret, and he becomes bitter at the Jedi for having fought alongside them in battle and then been expelled once the war was over. Something like that.