Please refer to the following in checkboard function in board/freescale/ls1046ardb/ls1046ardb.c in u-boot source code.
int checkboard(void)
{
static const char *freq[2] = {"100.00MHZ", "156.25MHZ"};
......
puts("SERDES Reference Clocks:\n");
sd1refclk_sel = CPLD_READ(sd1refclk_sel);
printf("SD1_CLK1 = %s, SD1_CLK2 = %s\n", freq[sd1refclk_sel], freq[0]);
return 0;
}
The value of sd1refclk_sel is read from CPLD, however you didn't program CPLD firmware on your target board, so the variable sd1refclk_sel is 0, SD1_CLK1( freq[sd1refclk_sel]) is freq[0], it is 100MHZ.
So, please program CPLD and FPGA on your custom board.