--I think,I found what is missing(but not tried yet) .
clk_config(CONFIG_REF_CLK_FREQ, 1000, CPU_CLK);
which is called in board_late_init function() .
I commented out this part because it seems to be related to the PMIC voltage setting.
--But clk_config () is called four times in imx53_evk to set NFC CLK,DDR CLK,CPU CLK ,PERIPHERAL CLK
for other mx53 boards its called only once for CPU CLK ?