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The All Blacks are legally bound to say little while the appeal is being conducted but it is believed they are unhappy with the way the IRB has handled itself.
Thomson, who was yellow carded and then cited at Murrayfield for standing on the head of Scottish flanker Alasdair Strokosch, has become a pawn in a much bigger power struggle.
The All Blacks have suspected for several years now that when they play in the Northern Hemisphere they are victimised by a judicial system that feels pressured by a rabid media and high-powered administrators. There is ample evidence to support their belief - none more convincing than the direct involvement of IRB chief executive Mike Miller in 2009 over a high tackle committed by Daniel Carter in Cardiff.
The All Blacks understand that Carter wasn't originally going to be pursued by the citing officer until Miller intervened. Their dismay grew in 2010 when England hooker Dylan Hartley wasn't cited for a rash, off-the-ball attack on Richie McCaw while Keven Mealamu was for a lesser incident on England's captain Lewis Moody.
The latest episode with Thomson has enraged the situation further as the initial judgement was barely released before new IRB chief executive Brett Gosper had used social media site, Twitter, to claim the case would need to be reviewed.
He appeared to be responding to earlier Tweets from Daily Telegraph columnists Mick Cleary and Brian Moore who both admonished the sentence as too lenient. It didn't help that a few days later, another prominent writer, Stephen Jones, tweeted that he'd just finished an excellent luncheon with Gosper.
Maybe it is All Black paranoia, but it doesn't feel much like it after reading the IRB's statement justifying the appeal.
"After careful consideration and having reviewed the full written decision in the Thomson case well within the permitted 72 hours of receipt, the IRB strongly believes that the sanction of one week is unduly lenient for this particular act of foul play and not aligned with the sanctions handed down in similar cases.
"The IRB firmly believes it is in the best interests of the game and its integrity to exercise its ability to appeal the Thomson decision."
The All Blacks withdrew Thomson from selection for the Wales test and are waiting now to hear when the appeal will take place.
The appeal decision will be final and binding, denying the All Blacks the opportunity to reiterate that the IRB's own recommendation for the foul play committed by Thomson is a two-week suspension when deemed to be at the lowest level of the scale - which they argue it was.
That suspension can be cut in half depending on mitigating circumstances such as previous good behaviour and intent. The All Blacks are adamant that due process has been followed and that there are previous cases in law this year which are in line with the punishment handed down to Thomson.