I solved the problem: pps was configured to generate very small pulse every second and my oscilloscope was not able to detect it.
I modified the file drivers/net/ethernet/freescale/fec_ptp.c replacing FEC_HIGH_PULSE with FEC_TMODE_TOGGLE in fec_ptp_enable_pps function in order to generate a square wave.
However, I have got a last question: is there a mannere, also by modifying fec_ptp.c file, to reduce the pps periodicity, generating a square wave of a lower period (i.e. 1ms period)?