I've been auto-connecting to a particular channel for over a year, but sometimes it doesn't auto connect me to it. When I manually join it, the "auto-connect" box is already ticked. When I untick it, it says it's saving channel to auto join list, but then when I tick it, it says it's removing it (ie it's opposite).
It's known bug and as far as I know S2 is working on fixing this issue.
Try right-clicking on the button to clear all previous auto-connect channels and then manually re-add each channel you want to auto-connect to. It's a little bit of a pain, but that should get rid of any oddities that may happen temporarily.
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