The Presidential elections in Afghanistan are key to the stability of the country, and in the fight against the Taleban and foreign militants. Afghanistan and border regions of Pakistan hold the key in the fight against global terrorism, and ensuring that there is an effective Government in Afghanistan is an integral part of that battle. However, this is easier said than done, and there have been a series of bad decisions taken in the past that have made things pretty bad right now, to the extent that the Taleban, which seemed defeated in 2001, is now resurgent and is control of an increasing large section of the country.
Hamid Karzai became the President when the country was removed from the grip of the Taleban, and over a period of time, the hopes and promises from Karzai have gradually decreased, to the extent that there is now a distance between the US administration and Karzai. There is less public support for Karzai from Obama and his team, and Karzai also openly condemns the US when there is some bombing or other steps that kill civilians.

In the midst of all this, there were the elections that took place. These elections were fraught with allegations of fraud and malpractices, with the contender, former Foreign Minister Abdullah Abdullah claiming that Karzai had taken a number of steps to influence people to vote for him, and during the time of elections, there was voter fraud. These charges have been repeated often enough that the election was seen as disputed, even though Karzai claims that he won the election and there was no need for a runoff.
However, it now seems that Karzai has accepted that the election was not as straight forward as he initially stated, and that he has agreed to a run off (even though the article states that it was not easy to get Karzai to agree to a run off) (link to article):

It had been hard to get President Hamid Karzai to accept a run-off, he said. Earlier, there were indications that Mr Karzai and his rival Abdullah Abdullah were discussing a power-sharing deal. The UN meanwhile announced that 200 top officials who had allegedly been complicit in electoral fraud in August were being replaced.
In an interview with the BBC’s Lyse Doucet, Mr Eide admitted that there had been difficult days of discussion in Kabul to convince President Karzai to accept a second round vote on 7 November.