WoW Update numbers mixed with ESO
 

Top image: I start Minion and there are 3 updates for ESO addons. Also many updates for wow addons I don't want to make so I only download the ESO addons. The WoW number stays at 31 after updating the ESO addons.

Bottom image: I closed Minion and opend it again now WoW displays only 29 AddOns to update but I haven't updated any wow addon.

Saw this problem many times now to thought I shoud share it.

Was it properly marking the ESO addons that needed updating in the first picture? Or was it saying those needed updates even though they didn't?

I think something goofy is going on in your detection cache thats in the minion.xml. Maybe rename your minion.xml and restart Minion so it can make a new one. This will reset Minion and force it to re-detect everything. If it doesn't work out you can always put the old minion.xml back in place.