For too long I had a problem with the Z-ordering of ComponentWidget's in VisualLibary.
As a reference it was fixed in NetBeans 6.8 (see http://netbeans.org/bugzilla/show_bug.cgi?id=169373 and the fix source in http://hg.netbeans.org/main-golden/rev/da7547f37f44).
As I am still in NetBeans 6.5 the solution was simply the use the 6.8 jar of the org-netbeans-api-visual.jar and replace the one in your Nb 6.5 install under platform9/modules.
Note that you CANNOT use the version from 6.9 or later due to some major refactoring of modules (like the Lookup got its own module).
This now works perfect.