After reviewing the datasheet, it looks a lot like your system is going into burst mode at low loads, as shown at the bottom of page 5, and described on page 12. It may even be "locked into" burst mode for some reason.
However, it isn't at all clear why this is happening, since you seem to have all of the mode pins configured correctly. But this is the area I would focus on.
Just as a side note, your question is really way too long, with a lot of information that may or may not be relevant. It would be really helpful if you would eliminate all of the PCB layout diagrams (until asked for them) and focus on giving us a clearer description of what the scope waveforms represent.