I've had this problem in the past and had forgotten about it until today when I decided it was time to try a new skin.

Currently, I'm seeing this on Vienna (XP). When I move my cursor, it moves underneath the window frame and/or title bar on all windows, even windows without focus in the background.

It could be linked with transparency. I've never seen it using Aerial in WB 4.x mode.

I'm using:

WinXP
WB 5.5
IP 3.2
OD+ 1.9
CursorXP (Free) 1.31

As I write this, I'm also noticing the same behavior on my ObjectDock tabs. With these, though, I can click on them to regain focus and I no longer go underneath them. No way to do that with the WindowBlind skins.

WindowBlinds version : WindowBlinds 5 (5.5 (build 94 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.
(Plug and Play Monitor) 1 is attached to NVIDIA GeForce 6800 GS

Wblind.dll      2007/03/13 10:50:20
Wbsrv.dll      2007/03/13 10:57:52
Wbconfig.exe      2007/03/13 10:16:17
Wbload.exe      2006/03/13 17:54:14
Wbhelp.dll      2004/09/18 16:37:07
Wbui.dll      2005/12/06 21:29:06
Tray.dll           2006/04/28 18:26:49