First off, when you open an application, If you click on the "Maximize" button does it still appear behind the taskbar panel?
Second,If you go to kcontrol->Desktop->Panels and select the "Hiding" tab, is there a circle in the option that says "Allow other windows to cover the panel" ?
If there is then there shouldn't be. The option "Only hide when a panel-hiding button is clicked" should be selected.
Third, If neither of these two fix it then I suspect it's a problem with compiz-fuzion. It is still in alpha stage (I think, or maybe beta stage). I'm experiencing a lot of annoying problems at the moment with kde and compiz-fusion.
All the best