The lower version is what is in the <addon name>.txt file located in your AddOn folder for that AddOn currently on your hard drive. Is your version set to v0.0.12 in your Undiscovered.txt?
The Red number is what is coming from us. Its trying to match it to the main version of Undiscovered and since there are 3 separate versions of Undiscovered virtually indistinguishable by looking at file structure Minion is picking the main download and not the patch. To fix this you'll need to un-install and re-install the one you want. Then Minion will track the correct one until you delete your minion.xml (that is where the addon detection relationships are stored).
Minion currently isnt smart enough to tell what version number is higher, only that they are the same or different.
http://www.esoui.com/downloads/searc...h=Undiscovered
About the initial startup after update, we are currently trying to track down a bug that makes this fail (has a less than 1% chance in happening). Simply restarting the app again will allow it to work again, as you have done.