Have been using the jobconfigurationhistory-pluging for some time and first ran into this ussue when having to create a new branch of jobs.
Use the folder plugin to keep some order in my jobs. then when starting a new test branch i use a scripting console job that itterates throug a folder copying all jobs to a new folder and updates the downstreamProject of the new job to point to the new job in the new folder.
There I saw that several projects had not updated some of the settings that had been updated in the old folder. (these changes may have been changed using the scripting console)
Then lated when copying a job without using the scripting console i saw the same issue. Again the changes that were missing may have come from a bulk update using the scripting console.
scripting console groovy to do change and copy jobs attached