I had the exactly the same issue with the WindowBlinds update this time (on Vista64bit too).
I can't remember how it was last time, but this time I updated WB and after the next reboot, Vista started with the classic (aka Win98) "skin", and with the WB-control panel open.
Whenever I tried to apply a skin nothing would happen at all. The only way to resolve the problem was to uninstall WB6 - reboot - and reinstall WB6. Rolling back to a previous version of WB didn't resolve the issue either.
I have the same problem with XP. Upgraded from WB5 and saw Classic skin, none of the other skins worked. Uninstalled and reinstalled WB6, but did not help. Got fed up and reinstalled WB5, but still the same problem. WindowBlinds version : WindowBlinds 5 (5.51 (build 97 x86))
WindowBlinds is installed correctly on this PC
WindowBlinds appears to be activated on this PC
Your machine supports per pixel borders on WindowBlinds skins.
(LG StudioWorks/FLATRON LCD 570LE) 1 is attached to RADEON X800 Series
(Plug and Play Monitor) 2 is attached to RADEON X800 Series - Secondary
Wblind.dll 2007/06/19 10:39:20
Wbsrv.dll 2007/03/13 10:57:52
Wbconfig.exe 2007/06/19 10:43:03
Wbload.exe 2006/03/13 16:54:14
Wbhelp.dll 2004/09/18 16:37:07
Wbui.dll 2005/12/06 21:29:06
Tray.dll 2006/04/28 18:26:49