Kamidan,
You should say whether or not you have auto-taskbar hiding on or not and what setting you have for "Show taskbar buttons on" in the taskbar properties. Personally, I'd just set it to the default Windows theme and see if it still does it. One thing I would wonder is are you using DisplayFusion, UltraMon, or another multi-monitor program?
DisplayFusion works well enough as long as you don't use their custom taskbar. It's got a feature on it called "Highlighted Buttons Flash Until Focused" that sounds somewhat like what you're describing and since in all this time of programming it they have barely made it past the feature set of UltraMon which hasn't been worked on in forever, I don't doubt this would break as well. Their way of adding taskbar icons makes me want to bash my head against the wall. I finally had to disable their taskbar since it assumes taskbar button heights are a always a certain size instead of just querying them, making it incompatible with WB themes.
Anyway, sorry to go off on a rant. 
