Events in Poland have left a deep wound and it has been festering away in Whelan's thoughts ever since. Yesterday, he chose to lance the boil and some plain speaking spilled out.
It should be noted that the presence of James McCarthy and perhaps David Meyler as a real threat to Whelan's position as one of Trapattoni's top men is clearly an irritation.
"The grass isn't always greener," was his assessment of the popular movement towards McCarthy as a must pick for Trapattoni.
But he will deal with that in his own way. He has battled the odds throughout his career and won more than he's lost.
He took as much criticism as anyone in Poland and this was his first real opportunity to address it.
His words do not read well for Ireland's manager. There is no glowing endorsement for Trapattoni, just a cold 'managers come, managers go' view of the current circumstances.
He will probably be used as a stick to beat Trapattoni in the coming days but that would miss the point. All Whelan did was repeat what he has been saying all along.
He did it first in the early days of Trapattoni's time when the RTE panel, then minus Liam Brady, judged the Whelan/Andrews midfield partnership to be inadequate.
Whelan didn't flinch and answered his critics with the truth.
To paraphrase: "It took long enough for me to get a cap, I'm in the team now, Trapattoni is the boss and I do what he tells me to do or he'll get someone else to do it."
It was a rational approach to a difficult situation but he went further and explained that modern football was moving in a certain direction and Ireland were set up to play a game from a decade ago or more.
He said it after Moscow when, like several other players, he pointed out that Ireland had been overrun in midfield.
It is odd that Whelan's voice has consistently identified Trapattoni as the reason why he and Andrews have suffered so much abuse, yet it has never become a major issue.
Shane Long said "I'm fit" and he's an idiot. "Whelan blames manager for Ireland's tactical naivety" - not a murmur.
Whelan clearly feels a personal responsibility for Ireland's collapse in Euro 2012 and it is obvious that he has no explanation for it. But he is not inclined to sit back and allow McCarthy and Meyler to take his place without a fight or to take the blame for mistakes he didn't make.
That's why this was a very bad interview for Trapattoni. Whelan's loyalty is to the shirt and whoever happens to wear the manager's cap, not the man.
He also laid down a challenge to McCarthy and Meyler and it would be a foolish punter who would bet against him starting against Sweden and Austria in March.