I sometimes have this happen, but not always. It's one of those odd little things that you can technically ignore.... As far as I know its only a visual thing.
It's the same as it was in 1.1.3. Home shows disabled add-on as unchecked, while the List Add-ons shows disabled add-ons with a strike through line across it (as there is no check box on the left side of the add-ons to dictate it's state). I think this is by design.