We have a board shows much higher ripple voltages on 3v3 supply. Ripple voltage of 270mV (pk-pk) seen with 5A load. On normal good board, it is less than 100mV. The ripples on 5V supply also bit higher than the normal.
I looked bit further into this and found the switching frequency is half of its intended. It switches at 250KHz instead of 500KHz for the 3V3 generation. The frequency selector resistor (RF) is 200KOhm and it should operates at 500KHz with this value.
I changed the RF resistor to 330K and it changed the frequency to the expected 300KHz.
On the 5V, it switches at 500KHz and 250KHz on alternate pulses.
I am not sure what is causing this. Initially I suspected the skip-select function (ie skipping 1 cycle make 500Khz to 250KHz). But it looks like this is not the issue as I disabled the skip-select, and still the controller operates at half rate for 3v3 generation.