The latest indications came following Wednesday's reported 'peace deal' between Shoaib and PCB chairman Shaharyar Khan which said the Rawalpindi Express may be let off with a mild reprimand or warning.
"There is no doubt that he (Shoaib) is carrying an injury. But the medical commission has given its report to the chairman after studying videotapes of the players including Shoaib's batting and bowling.
"They also spoke to related people on the issue. They have their views on how old the injuries are," Raja was quoted as saying by local daily The News, suggesting that Shoaib's injuries could have been sustained much before the third and deciding cricket Test against India last month.
Raja said PCB was not upset at the team losing the series to India but it cannot accept "the lack of effort shown by many of them in the Pindi Test".
"We are not denying his (Shoaib's) stature as a match winner. We are not questioning his cricketing skills. But one thing we want to make very clear to our players that while we can accept victory and defeat as part and parcel of the game, the sort of attitude and lack of effort shown on part of many of them during the final Test in Pindi will not be tolerated by us or the cricket loving people of this country," he said.
PCB also acknowledged that the medical inquiry commission had submitted its report on Shoaib and four other cricketers -- Shabbir Ahmed, Umar Gul, Moin Khan and Abdul Razzaq on Wednesday. But the report has not been made public.
However, the bone scan report on Shoaib leaked to the media said he has a stress fracture on one of his ribs.
The fast bowler had earlier planned to address a press conference and later approach Supreme Court against the PCB for defaming him. But after Wednesday's meeting with Shaharyar at Lahore he declined to speak to the media. He, however, admitted that he was asked to remain silent by the Board.
Raja said Shoaib would be given the message that this was the last chance for him to change his attitude because the captain was the sole authority in the team and he has every right to feel dejected and let down, if his senior players didn't show the required passion and purpose in their game.
"We could have settled for batting on more placid pitches against India and gone for draws. But we relied on our strength that is our fast bowling and it was disappointing for all of us the way they didn't come through on responsive pitches.
"We can understand Shoaib being concerned because he has a contract with English County Durham about which he has not spoken to us as yet," he said.
Raja said the Board's credibility suffered because it prepared fast pitches for the India-Pak matches keeping Shoaib in mind. "Our credibility is being questioned after the way we lost the Rawalpindi Test to India because of the lethargic attitude of some players."