At first the Doctor didn't realise what the Master was doing, not really anyway.
He'd put the Masters actions down to his troubled mind, he'd given the Doctor enough proof of that over the years.
The second time the Master did it, the Doctor let it slide.
The third time the Doctor started to doubt his reasoning.
By the fourth time, he'd worked it out.
After all, what better way to get someone's attention than take over their favourite planet?