In the last several releases I notice that the Renumbering wizard isn't resetting the counter for each directory when selected. I believe it has to do with the files being sorted out of order due to the same filenames in different directories.
If I name the files in two directories with the same file names, i.e. Track1, Track2 in Directory1 and the same names in Directory2, then the problem occurs.
If I rename them to be something like Track1-1, Track1-2 in Directory1 and Track2-1, Track2-2 in Directory2, then they sort correctly and it renumbers correctly, resetting the count when it changes directories.
Hopefully this is clear enough for you to duplicate. Unfortunately I don't know what release changed this behavior, but it used to work regardless of the duplicate filenames and as mentioned, has not functioned properly for several releases.