Have you run the explorer shell without running WB5 yet to test?
If shell runs without WB5 applying a skin, you might try applying a skin > apply one of the Windows defaults using WB5 > reboot > apply the Windows XP theme via "Display Properties > Themes tab" > reboot > apply the skin you want using WB5 and reboot to test.
During some 10-12 testing procedures which included "Installing/testing/uninstalling/clean install of OS/clean install of WB5" on both a notebook and homebuilt desktop - I have found that the first time WB5 applies a skin after installing, and the subsequent unloading of WB5 can result in strange behavior in either the Display Properties dialog, or in explorer shell. When this happens (not a consistent issue), I have found that rebooting and successfully restoring the default Windows XP theme, and then reapplying a skin using WB5 has always cleared the issue.
I also saw the shell resizing (maximize and restore) having some slow redrawing after the current (RC), and then it improved for some reason which is not clear to me. The shell resizing behavior reminds me of when I was running a PC with onboard graphics, and running ObjectDock with magnification on.
I currently run ATI Radeon X700 Pro (256 MB) AGP and the 5.11 display drivers on the desktop, and have found the redrawing in 4.98 beta seems to be better than the new 4.99 (RC) - though I have not had time to fully test, and the official release will be out next Tuesday - so I will probably just hold off on testing.
Another option would be to download say the 5.9 drivers, as well as the uninstaller utility from ATI web site, and uninstall the 5.11 drivers > reboot > install the 5.9 drivers and then test the shell.
Not knowing the program from a coders' point of view, I do not have any suggestions for manipulating files or settings to fix the issue, so that is it for me. 
