Massive cross-voting in Karnataka helped Mr Mukherjee get 53 per cent of the vote from that state. He polled 117 votes, against Mr Sangma's 103. Mr Sangma, the BJP's candidate, should have got 116 votes, taking into account that allegedly three BJP votes were found invalid. And Mr Mukherjee expected 98 - 71 from Congress MLAs and 27 from the JD(S).
Red in the face, the BJP will also now have the task of finding out which 13 MLAs cross voted. Difficult, say party sources, in a secret ballot.
The party only recently gave in to pressure tactics from the Yeddyurappa camp and, it said, electoral imperatives, to make Lingayat leader Jagadish Shettar Chief Minister. But that meant angering another powerful community, the Vokaligas, since the man the party unseated, Sadananda Gowda, belongs to that community. Was it a section of unhappy Vokaligas that revolted?
Was it the group of MLAs from the Bellary region, close to jailed mining baron Janardhana Reddy - who seemed to form a separate block when it came to recent negotiations?
Or was it one of quite a few BJP men who are said to be unhappy at not being included as ministers?
Then there is that statement of party strongman BS Yeddyurappa that will no doubt play out in the minds of many. Quite the law unto himself, Mr Yeddyurappa had said in an interview to NDTV recently that he believed Mr Mukherjee was a good candidate for President, but that as a loyal party worker he would vote for the BJP's candidate.
Mr Yeddyurappa is the man who scripted Mr Gowda's exit. A year ago he had handpicked Mr Gowda to replace him as Chief Minister, when he was indicted by the state ombudsman in cases of illegal mining and had to step down. He believed he would be back soon and said as much. But when Mr Gowda seemed to have become his own man in a few months, Mr Yeddyurappa began the clamour for his ouster. He is supported by a majority of the BJP's MLAs and as such is still seen as the most powerful leader in the state. Once it became clear to him earlier this year that he wouldn't be back as CM any time soon, he began to demand that Mr Shettar be made CM.
Karnataka watchers say there is no guarantee that he will not demand Mr Shettar's exit soon.