I've seen this as well, but without using a Start Menu docklet. It has happened when using the normal Start Menu.
What seems to trigger it is when I get my cursor too near the dock while traversing the program menu list. As soon as the dock (the zoomer dock, not tabbed) starts to grow, the Start Menu covers the program list.
And to add the the oddness, I still get the mouseover for the program menu items behind the Start Menu if I move my cursor over their position; despite the fact that they are mostly obscured by the Start Menu.
Oh yeah, using XP Pro SP2 here also