I've been having a bit of discussion along these lines with SSWR.

Many cultures have an end of times myth that requires the coming of a special individual for the whole thing to kick off.

In the TPM the Jedi think they have already defeated the Sith so they rationalise this by thinking that prophecy may have been just a legend or may have been fulfilled in some unrecorded, symbolic or forgotten way (many Jewish people feel the current state of Israel is not the promised one because the Messiah didn't give it to them, some argue that the Messiah is the state itself returning, some say that the Messiah did turn up but his name wasn't recorded or that the Messiah aspect of the story is just a legend).

So when Qui-Gon announces that he thinks he has encountered a Sith Lord and the Chosen One it shakes them a bit.

I think it would shake them more if Qui-Gon claimed to have found the Chosen One first because the prophecy hinges on him bringing balance to the Force and destroying the Sith.

If they are so cock sure the Sith were destroyed long ago but the Chosen One has just turned up that would put the cat among the pidgeons for them, just as saying the second coming of Christ has happened to a believer of the Gospel of John.

The second coming is meant to be preceded by the reign of the antichrist which would mean the antichrist had been around for a long time already and they hadn't even noticed.