For the first time in the Blues boss’ 22-month tenure, he opted to line-up with a wing-back system at Stevenage on Saturday.
The outcome was a 3-0 defeat as the hosts recorded a ninth victory in 11 matches.
Pompey struggled to find their feet in the new formation, falling two goals behind after 28 minutes.
Stevenage ran out deserved winners to cut the Blues’ lead in third spot down to four points.
Cook’s team selection was influenced by the injury absence of Kyle Bennett and Kal Naismith.
But he was not keen to discuss the subject in the post-match press conference.
He told The News: ‘I am not going to debate system changes.
‘We had players on the pitch, we’ve had two players who failed fitness tests, so had to make some kind of changes.
‘We did that and when you have results they are always deemed to be good changes or bad.
‘I am not going to get involved. I will tell you that another day when I am in a better mood.’
Cook, who lost Christian Burgess to a red card with 15 minutes remaining, did, however, touch upon the system question in a radio interview.
He added: ‘We picked a team we felt could score at one end and manage to keep clean sheets, unfortunately it never worked and that’s the game.
‘When you change formations you change for a reason.
‘We went with three strong centre-halves because we wanted to defend early on, we felt our substitutions late in the game could help us win.
‘But the game was done and dusted by 46 minutes.’