Is that saying job editing used Add filter of Exclude folder with value /root/.config/Duplicati/ or that Commandline screen shows that value? If it shows an --exclude of */root/.config/Duplicati/*/ I think there may be a GUI entry bug that makes Exclude folder dropdown treat your value like Exclude directories whose names contain dropdown. If one goes back to look at Filters, that’s what’s shown.
One can click the three-dot-menu, or switch screens to adjacent screens 2 or 4 then back, to watch the dropdown change. Setting the dropdown again can make it stay put. Three-dot menu can confirm results.
Another possible point of confusion (for those who read the documentation) is that it’s not clear if a trailing slash used to imply folder is supposed to be entered for a folder dropdown, or if it’s added automatically.