It's definetly worth looking into in the future.
What I think is happening is that when you hide the taskbar, a new line of "blocks" opens. When you place an icon into one of them, and then activate the taskbar, it's then impossible for the icons to remain in the position they were, thus they shift up one block to make way for the taskbar.
However, the system still registers the icons as being in the previous position, so when the bug happens, they still "shift up" a block, but on the desktop they remain in the same position.
In other words, I think the problem doesn't disappear with this "fix", it just gets masked because of how the extension works.
But then again, these are just speculations, and I have no idea how extensions work 
By the way, now that you say it, I remember seeing something about a race condition related to this problem. And I just realized it was your comment 