Wow, I never even noticed these changes. Maybe - after the painful events at the end of HLV - Mycroft was (purposely or subconsciously) trying (not very successfully as far as Sherlock is concerned) to distance himself even more from anything that could be even remotely close to friendship or caring (feelings which - according to him - could only lead to pain in the end). Thus the more formal, distant addressing of John.

But In TFP Sherlock and John are quite close again, working together all the time, even creating the horror house scenario for Mycroft. But even after Sherlock expressly states that he regards John as family, Mycroft continues to address him as Doctor Watson. 

He calls him Doctor Watson all the time in this episode - in the horror house, in 221b, and in Sherrinford in more than one instance. 

If it's not because Mycroft tries distancing himself from everything that could be too personal, then it could also be a sign of respect: At the end of TAB he kind of officially passes the "durty" (or priviledge?) of looking after Sherlock on to John ("look after him, please"), he entrusts John with Sherlock's safety and wellbeing. So the "Dr. Watson" could also be a sign of respect, showing that he thinks John worthy to take over that task. 

In TLD we see Smith questioning John's doctor title and we see John reacting badly to it. It seems that his title is important to John.

Maybe Mycroft saying "Dr Watson" is the reversed action to that, a display of respect.

Maybe.  May well be.  That's good of Mycroft, if that's the reason.  I like that better than Mycroft using John's title to distance himself from him.