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DP83640: Step Adjustment and Direct Time Set

Other Parts Discussed in Thread: TMS320C6454, DP83640

I'm using a hardware which interfaces DP83640 to TMS320C6454 processor.

I'm referring to PHYTER Software Development Guide Ver 1.97 for developing software. 

For synchronizing DP83640 PTP Master to a GPS Receiver (referring to application note snoa548a), I'm doing a direct time set operation using the following code snippet:

void
    PTPClockSet (
        IN PEPL_PORT_HANDLE portHandle,
        IN NS_UINT32 numberOfSeconds,
        IN NS_UINT32 numberOfNanoSeconds) 

This code execution results in rapid pulsing at the PTP PPS output. Why does this happen? How should the initial large offset be corrected by avoiding the rapid pulses at PPS output?