There was rigging in Karachi even in 2008 but no one took any action. There has been rigging in Karachi in 2013, but no action will be taken. It was reported on TV that Chief Election Commissioner himself called Corps Commander Karachi and Army chief, requesting them to post military personnel on polling stations in karachi but they refused. Makes it pretty clear that they wanted to give MQM a free hand.
By boycotting the elections in Karachi, JI and other parties had already built momentum for re-polling throughout Karachi. But over zealous PTI supporters diverted the pressure that was building against MQM by holding dharnas in Lahore and Islamabad calling the election results there as rigged.
This gave the impression that PTI was a sore loser because polling stations in Punjab were open to media and foreign observers and no one reported serious rigging. If PTI had kept focus on Karachi where the actual rigging had taken place and had joined other parties in the demand for re-polling all over Karachi, it would have become a strong issue. But now, due to immaturity of PTI leadership, no one will take these rigging allegations seriously even in Karachi and we'll end up with re-polling only in NA 250.