I've been using Bagnon forever and only recently started having this issue sometime after updating to the latest build.
I always had my items sort in the order filled bag spots --> empty bag spots, on every toon. I signed in one day and my items were sorting in empty slots --> filled bag spots, so I looked in the settings and tried checking "Reverse bag order". That fixed it, great! Except then I signed onto my other toons... those were all sorting backwards. So I checked or unchecked the setting for "Reverse bag order", depending on whether it was previously checked or unchecked. Again, that worked.... on that toon. Every time I log in to another toon, I have to change this setting AGAIN. It's getting really frustrating and I don't have any other bag addons, and I disable ElvUI's bags/bag sorting because I don't like their windows for it. I did even try changing settings in ElvUI and it had no impact.

Go to the blizzard default options. There are options there regarding sorting order, you probably have them differently on different characters