Is it permissible to pay Zakat on money with a certified check deposited into the Zakat Fund's bank account due to a lack of liquidity and limited available withdrawals?

There is no harm in paying Zakat (definition) by check to the Zakat fund if the fund is able to cash it and disburse the amount to its rightful recipients. However, if the fund cannot cash the check immediately due to a lack of liquidity, this delays the payment of Zakat, which is obligatory immediately once its conditions are met. If you are able to pay it in cash instead of a check, this is preferable. Otherwise, you are excused for the delay due to the lack of liquidity.