Minion remembers the latest version it downloaded for each addon. It doesn't check each addon's *.txt file in your Addons folder for the current installed version.
For example: if I work on my addon and increase the version number, place it in my addons folder, and then upload it to ESOUI, Minion will still "update" my addon even though the files it downloads are identical to the ones I already have.
I also work on my addon directly in ESO's addon directory, but haven't had any problems yet
