I've cleared the addon cache which sometimes fixes it for a bit then it comes back confused.
Addon authors putting "3.06.15" in the version field and 30615 in the .toc (I'm looking at you Arkinventory) or "2.5.0 - r188" in the version field and "2.5.0-r188" in the .toc (lookin' at you, Elkano's BuffBars) are bad enough, leading Minion to constantly think an update is needed (for which I really wish there was a 'accept wow-interface ver as proper until it changes' option) are bad enough w/o Minion coming along and helping addon authors confuse the poor, downtrodden user. There's only so many nights you can fruitlessly sit up in the dark waiting for the underpants gnomes to rearranged your installed addons before you start thinking it just might be a software issue and the gnomes are (shockingly) blameless.
So you're saying even though you've installed those AddOns using Minion some times when you load up Minion it pairs them to a different one? I just want to make sure you haven't deleted the minion.xml or anything when this happens have you?
Would you be able to post your minion.log when this happens?
Thinking about it more I'm betting there is an AddOn folder Minion is having trouble identifying so it keeps trying to re-detect and match it to something. The log should shed more light on this.
PMed it to you w/ a list of the actual addons I'm using.
I cleared the detection and opened it a couple times...sometimes Dominos Beta shows, sometimes no Dominos at all... not the only addon that does that now that I think about it, ArkInventory (which I notice b/c of the aforementioned .toc/wow-ui version issue) is displayed intermittently as well.