To clarify, this is the ‘Mark all as read’ button that appears when you hover over the area that is above the list of stories (below the reading pane on the right side). I’ve seen this in FF 15 as well.
In the meantime, I’ve been using the keyboard shortcut Shift+A or using the ‘Mark as read’ item in the menu (from clicking the triangle to the left of the feed name).
I’ve been experiencing the same issue on my touchpad…figured it was just due to the quirkiness of the platform. I’ve confirmed the same behavior in chrome 21.0.1180.83 on win 7 x64.
Whew, fixed that. Sorry about the lapse. It happened because I fixed right-clicking, in the process breaking the mark as read button. You can also use shift+a to mark as read (as well as the menus).