We have had a number of customers confused by small discrepancies in the tax they have paid based on the IR348 and the amounts posted to their financial systems. This discrepancy is caused by ESCT. In April 2012, the 2% threshold on Kiwisaver contributions was removed meaning that there is now an ESCT component to what employers pay the IRD (see http://support.flexitime.co.nz/entries/21046877-esct-changes-april-2012).
Prior to April 2012, the total shown on your Employer Monthly Schedule (IR348) would generally be the amount owed to the IRD. However this IRD form does not show ESCT. The reason is that the IR348 is a record of tax paid per employee, whereas the ESCT is considered by IRD to be a payment from the employer, and they seem to have no interest in which employee the ESCT is deducted for.
The Employer Deductions (IR345) is the correct place to look to determine the amount of tax you need to pay. This should be filed with the IRD along with your IR348. With FlexiTime it is a simple as downloading and uploading the file to the IRD website.
The IRD have created this video to explain ESCT.