A well-informed source in the board told PTI that Younis Khan's press conference on Monday had set the alarm bells ringing in the board.
The senior batsman vented his frustration at not being part of the one-day squad and said he was shocked at his ouster as he had not given up on playing one-day internationals.
"The board hierarchy is not happy that in recent days some contentious statements have come from the national team even though players and officials are strictly bound by clauses in their central contracts to avoid speaking on contentious issues," the source said.
"Apparently the board also took notice of Whatmore's comments on a television show that there was a lack of nationalism in Pakistan cricket when compared to other cricket playing like India, Sri Lanka or Bangladesh in the continent.
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"Whatmore then also decided to air his displeasure over Ajmal's comments on his coaching on twitter and this also didn't make the board happy," the source said.
He said Ajmal's comments about foreign coaches and Whatmore had put the board in an uneasy situation before the SA series and that is why it forced the senior player to apologize to Whatmore and also posted a press release about this.