Hope this helps:
SIM_SOPT2 &= ~SIM_SOPT2_TIMESRC(3);//clear
SIM_SOPT2 |= SIM_SOPT2_TIMESRC(1); //PLL clk
// Program INC and Period Regiser
ENET_ATPER /*(mac_sel)*/ = 0x3B9ACA00; //10^9
//Using PLL/FLL clock
ENET_ATINC/*(0)*/ = ENET_ATINC_INC(10) | ENET_ATINC_INC_CORR(10);//100MHz
// Enable Timer
ENET_ATCR/*(mac_sel)*/ = ENET_ATCR_EN_MASK;
Do not forget to set into Enhanced Buffer Mode (not legacy)!