The fade/mouseover option for bars is not working as of 2.1. If you mouseover the bar you still get the tooltip, but there is no icon.
I am also having this problem. What's interesting about it is that if you unlock the bars (and they turn green) then it *does* work properly - mouseover the bar and it appears, mouse away and it's gone. However, once you lock the bars you get the behavior that Killariel described - mousing over gets you the tooltips but the bar doesn't appear. Any help would be greatly appreciated!
P.S. I am not using AutoBar.