Juan Cole has a bead on it:
There are two electoral commissions operating in Afghanistan, a wholly local and a partially international one. The local one, the Independent Electoral Commission (IEC) of Afghanistan, announced Tuesday that with 90% of ballots counted, incumbent President Hamid Karzai now has 54% of the votes, enough to allow him to avoid a second-round run-off against his chief rival, Abdullah Abdullah. But the other body, the United Nations-supported Independent Electoral Complaints Commission (ECC) (which has Afghan members but the head of which is a Canadian), clearly was disturbed at the IEC announcement and it ordered the IEC to conduct a recount and to throw out clearly fraudulent ballots.
In essence, the two electoral commissions have locked horns, and if the local body gets its way, Karzai may well be declared the winner hands-down. The UN-backed Electoral Complaints Commission has the authority to order recounts, but it is probably too under-staffed and under-funded to make its objections stick. If the IEC declares for Karzai, he may well keep his job because of inertia (see: next-door Iran). On the other hand, the EEC’s objections really could lead to a massive recount of over 5 million ballots, which might delay a firm result for several months.
I doubt the analysis that the EEC is “probably too under-staffed and under-funded to make its objections stick.” It is very likely under-staffed and under-funded, a weight too many UN offices are forced to suffer under, but people seem to be listening to what they have to say, and I very much doubt that the Karzai government could just sweep those objections under the rug.
What does “UN-supported” mean? According to the EEC website, it was formed under Article 52 of Afghanistan’s Electoral Law and three of the five EEC commissioners are chosen by the UN Secretary General’s Special Representative. Those three commissioners –Maarten Halff, Scott Worden, and the chairman Grant Kippen — look pretty impressive, at least on paper, having served in election monitoring capacities in Algeria, Bangladesh, Cambodia, Iraq (where Halff “advised on the development of election laws, electoral systems and complaint mechanisms”), Liberia, Nepal, Moldova, Pakistan, Timor Leste and Ukraine.