I've got the exact same problem on my Vista 64-bit. Most boxes that I should be able to choose [x] enabled or [ ] disabled are not showing either. I loved the skin "Dragon (Vista)" and enabled it, then many windows-programs don't show titlebar, menue's, buttons. That incl. MSN, IE, Firefox, etc. I've even tried to reinstall WindowBlinds and change resolution from 1680x1050 to everything below that.
Your computer has a Windows Experience Index base score of 5.9
Your Windows Graphics Experience score is 5.9
WindowBlinds version : WindowBlinds 6.3 ( 61 x86) - 64 bit OS
WindowBlinds is installed correctly on this PC
WindowBlinds appears to be activated on this PC
(Dell E228WFP) 1 is attached to ATI Radeon HD 4870 X2
Wblind.dll 2008/10/18 15:55:20
Wblind64.dll 2008/11/06 12:22:13
Wbsrv.dll 2008/09/16 07:44:13
Wbconfig.exe 2008/11/18 17:15:54
Wbload.exe 2008/04/26 15:14:14
Wbhelp.dll 2008/04/26 15:14:07
Tray.dll 2008/04/26 15:14:21
Wbload.dll 2008/04/26 15:14:28