Question
Does Islam allow payment of zakat fitrah through cheque? And what are the implications if the cheque reaches Muis late?

• Yes, It allows because according to Islam, an individual that has reached nisab and haul, he is obliged to pay zakat through any means, be it he disburse it without any obliged party asking for it, or he passes it to the obliged party or he entrust somebody or a party to disburse it for him.
  
  With that it is clear that it is allowed to pay zakat through cheque because in this way, the bank help to give it to the obliged party. While you were writing the cheque, there is already an intention to pay zakat. You have not sinned if the cheque reaches late to Muis if it is not because of your carelessness.
  
  When you are doing your cheque, post order or others, the payer of zakat fitrah has to niat: "This is my zakat fitrah which is obliged upon me and by dependents, I am paying because of Allah Ta'ala." Or for niat zakat wealth: "This is my zakat wealth which is obliged upon me, I am paying it because of Allah Taala." The receiver is not expected to offer any intention. That is why it is no problem if the receiver is a non-Muslim.
  
• About zakat fitrah, if a person pays at the early part of Ramadan, usually it does not reach late but if a person pays at the end of Ramadan, maybe the cheque will arrive late. As long as he has already paid, it still considered as sah.