let us inform you that an amendment to the Payment System Act will come effective on November 1st, 2009. Based on this amendment, payments to the state budget (duties, taxes and fees, etc.) will be considered settled as of the day when the payments are received by the customs/tax authority.
In practice it means, that all such payments should be arranged in sufficient time (e.g. at least two days before the maturity from the domestic bank account in Czech currency).