I inspected your several last fonts and didn't saw any reasons to use the "pixel contour type" option which is default for now. It is a workaround which trace any shapes correctly but with a cost of increased file complexity. Your last fonts aren't affected by the bug so you can use normal "outline contour type" (maybe I overlooked some affected symbols ¯\_(ツ)_/¯).
To enable outline contours you need to press output->contour type->outline. You can see the difference in my previous comment where you see g from squares which is a result of pixel contour and another where you see solid shapes which is produced by outline contour.
Why it happened? I am not sure that but it looks like you just used the utility like before but in the update was added pixel contour type which is default from that moment...
I am almost sure I understood which symbols are affected (and didn't found in you last font such symbols) and even reason of the bug but we can't know it for sure because the app is proprietary and it isn't possible to just change the code and immediately see the result