One other thing.... I've noticed that when I make parameter changes using the new XCTU program that sometimes those changes do not go over.
For example I made a change to D3 and MY at the same time and clicked the write radio setting button at the top to write all changes. However sometimes the changes did not always go through (and I am using the Digi dev board).
If I made the changes using the write to radio button next to the configuration parameter it did appear to work fine since it only write that particular parameter over.
So just make sure your changes did indeed go through.