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We made it show the 2 pixel line to match the behaviour of the Windows taskbar. It's not possible to make it completely invisible, but on the DisplayFusion Settings > Taskbar tab, you can set the Taskbar Opacity to 1.
As for the taskbar not coming out of auto-hide, we've had a few other customers report the same thing, but we've never been able to find a consistent trigger that's causing it to happen. Quick question: when it won't come out of auto-hide, are you able to see the 2px line, or is it missing?