Very strange drizzane,
It sounds like you launched WOW while Minion was still detecting or updating the AddOns folder (best guess atm)? It's possible Minion locked the AddOn folder while it was trying to detect (or update) all your AddOns and then WOW tried to read from the folder and was told that folder is currently in use by another application. Thus making it look like ElvUI went away.
Try launching Minion and when its finished fully loading and doing any updates and sitting on the screen where it lists your installed AddOns then load WOW. Does ElvUI show up for you now?
If you could also provide your minion0.log and minion.xml files that would be great. If you're on windows they are located in the .minion folder under your windows user folder: C:\Users\<your windows username>\.minion. Those files will help me understand what Minion is doing on your computer.
Thank you for helping us beta test Minion.
