This happens with 0.62.1. I do not know if this has been fixed in the most recent alpha (i will be installing it later tonight to find out), so i apologize if this is old news.
i was toying around with the slit, and noticed that if i threw a large dockapp in there, it would bump up above the toolbar (which i believe is correct behaviour), but would overlap it by a few pixels (which i believe is not correct). Screenshot with xmag blowup: http://furt.com/blackbox/bb-slit-toolbar-overlap.jpg I will try out the latest alpha later today, and if this still happens, i will post to the SF bug tracker.