There were no third-party, independent accounts of the invasion - just the word of the ruler of a planet that was having a dispute with the Trade Federation. If we look a little further in the script:
LOTT DOD (delegate from the Trade Federation): I object! There is no proof. This is incredible. We recommend acommision be sent to Naboo to assertain the truth.
LOTT DOD: Your Honor, you cannot allow us to be condemned without
reasonable observation. It's against all the rules of procedure.
A third box representing Malastare moves into the center of the room. AKS
MOE, the Ambassador, addresses the convention.
AKS MOE: The Congress of Malastare concurs with the honorable delegate
from the Trade Federation. A commision must be appointed...that is the law.
Notice that nobody's saying that Padme's accusations should be ignored or forgotten, but that they must be investigated by an independent commission. Yes, such a commission would have found that the Trade Federation had invaded illegally - if it ever got off the ground, with Palpatine slowing everything down.
This is what was meant earlier in the film when Sidious was talking to Gunray:
DARTH SIDIOUS: Good. I have the Senate bogged down in procedures. By the time this incident comes up for a vote, they will have no choice but to
accept your control of the system.
Most of the evidence the Queen has with her could easily be fabricated; the only independent evidence she had was the testimony of the Jedi, and they weren't there. If she'd been thinking clearly, she probably would have called them, but she wasn't thinking clearly. She had been carefully prepped and manipulated by Palpatine:
PALPATINE: ...the Republic is not what it once was. The Senate is full of
greedy, squabbling delegates who are only looking out for themselves and
their home sytems. There is no interest in the common good...no civility,
only politics...its disgusting. I must be frank, Your Majesty, there is
little chance the Senate will act on the invasion.
AMIDALA : Chancellor Valorum seems to think there is hope.
PALPATINE : If I may say so, Your Majesty, the Chancellor has little real
power...he is mired down by baseless accusations of corruption. A
manufactured scandal surrounds him. The bureaucrats are in charge now.
AMIDALA : What options do we have?
PALPATINE : Our best choice would be to push for the election of a stronger
Supreme Chancellor. One who will take control of the bureaucrats, enforce
the laws, and give us justice. You could call for a vote of no confidence
in Chancellor Valorum.
AMIDALA : He has been our strongest supporter. Is there any other way?
PALPATINE : Our only other choice would to be to submit a plea to the
AMIDALA : There's no time for that. The courts take even longer to decide
things than the Senate. Our people are dying, Senator...more and more each
day. We must do something quickly to stop the Federation.
PALPATINE : To be realistic, Your Highness, I'd say we're going to have to
accept Federation control for the time being.
AMIDALA : That is something I cannot do.
Palpatine has prepared her to see the exact situation they do see - squabbling senators, no interest in the public good, a request that she delay and let her people suffer...so she moves forward with the dramatic move nobody (except Palpatine) had expected.
EDITED TO ADD:
I forgot to address this when I first answered, but the description of the Jedi's mission from the question:
The personal testimony of multiple witnesses, including two Jedi (who, as the opening crawl tells us, were dispatched by the Supreme Chancellor to investigate this very issue)
...is not correct. The opening crawl says:
While the congress of the Republic endlessly debates this alarming chain of events, the Supreme Chancellor has secretly dispatched two Jedi Knights, the guardians of peace and justice in the galaxy, to settle the conflict.....
The Jedi were sent to negotiate the end of the blockade, not to investigate reports of a Trade Federation invasion. The testimony of the Jedi would have helped strengthen Padme's case, certainly, but it would not have been the same as sending a commission specifically to see if there really was an invasion.