I am having this same issue but my issue seems to be related to RDP sessions..
Seems that when I log into my remote Vista Ultimate system at home from my work XP SP3 PC
the theme does not get applied, if I manually try to open the WBConfig it tells me I must
reboot after installing this version..

I reboot but still no theme and no WB idon in task tray, if I go home
and log into the PC locally I get the same issue no theme, manually open config
and it tells me to reboot, but this time when the PC reboots the theme comes
up and the icon is there..

I go to my bedroom (yes I have a laptop there) and log into my Vista Home Prem
computer and RDP into the machine in other room, I get no theme and we start the
loop all over..

It did NOT do this with all the 6.0X beta versions up till this one..

can any one shed some light on this...RDP is a must for me!

(when I get home, im at work now I will post all my details here cant get the
config to open in RDP now)

Edit:

Your computer has a Windows Experience Index base score of 5
Your Windows Graphics Experience score is 5.9

WindowBlinds version : WindowBlinds 6.1 (build 97 x86 - Vista Edition)

WindowBlinds is installed correctly on this PC
WindowBlinds appears to be activated on this PC
(LG L226WPA(Digital)) 1 is attached to NVIDIA GeForce 8600 GT

Wblind.dll 2008/05/06 15:25:20
Wbsrv.dll 2008/04/28 11:35:58
Wbconfig.exe 2008/04/29 21:02:32
Wbload.exe 2008/04/28 11:35:14
Wbhelp.dll 2008/04/28 11:35:07
Tray.dll 2008/04/28 11:35:21
Wbload.dll 2008/04/28 11:34:28
Screen.exe 2008/04/28 11:35:18