Ok, so this is just a visual issue in the Production view, right? I mean, the colonies are not really on Auto, they do not autobuild stuff, correct? As long as you don't click on the checkbox everything is good?
Since in your particular case you don't use Auto at all, it does not have an impact on your games?
Regardless, it is an odd issue and it should be traced and fixed. Just not sure how...
I'll try something in the next patch, but I'm not very confident.

