atomico & Nyro your minion.xml is a little messed up. It has 2 -3 games with the same unique id so it can't save addon information properly.
The issue was a game from the Minion game list was deleted and a new game was added. We currently have a bug when you remove game first then add a new one it will assign the new game the same unique id. We are working on a fix for this.
Best solution for you is to delete your minion.xml to reset minion. Then once more redownload the addons that are missing and it should remember them after that. When you delete minion.xml try not to remove any games, only add 1 game.
If your curious to see where the problem is:
See how these two games have the same unique-game-id?
Code:
<game addon-path="C:\Users\Atomico\Documents\Elder Scrolls Online\live\AddOns" auto-update="false" game-id="ESO" ignore="true" unique-game-id="ESO-1"/>
<game addon-path="C:\Users\Atomico\Documents\Elder Scrolls Online\liveeu\AddOns" auto-update="false" game-id="ESO" unique-game-id="ESO-1"/>
This one has 3 of the same
Code:
<game addon-path="D:\Nyro\Documents\Elder Scrolls Online\live\AddOns" auto-update="true" game-id="ESO" ignore="true" unique-game-id="ESO-1"/>
<game addon-path="C:\Boot" game-id="ESO" unique-game-id="ESO-1"/>
<game addon-path="D:\Nyro\Documents\Elder Scrolls Online\liveeu\AddOns" game-id="ESO" unique-game-id="ESO-1"/>
Hopefully we can get a fix for this bug soon but just removing the minion.xml should force Minion to reset. You'll have to download your missing addons once more but from then on it will continue to remember them.