I personally manually update my addons so have never used Minion myself so the following is based on what might be the case.
With the latest patch just a few days old with a new TOC version you might find that addons that are fairly up to date showing as out of date. If the addons are working as expected, then all is good, if they are not, maybe time to check the addon creator is aware of the issues and are seemingly dealing with the issues. Don't forget some people have full time jobs and may only get the opportunity to update their addons in their spare time.
As to the other client problems you are having. Maybe Minion checks the folders every time to ensure they are up to date to avoid having issues updating into a non existent folder.
Other than those possibilities, hopefully someone in the know will respond and/or are dealing with the issues already.