This is probably more for Neil (WB developer) than anything else.
I have done a clean install of the OS (both Windows XP Home and Pro) on my notebook and desktop - 3 times in the last week to test the installation and functionality of WB5 beta on my systems. I will list the Troubleshooting report text at the end.
I have used Stardock Central each time to install the programs I use: WindowBlinds, IconPackager, and ObjectDock Plus - all of which were reinstalled after each clean install of the OS.
Each time, I installed WB5 beta directly (no preinstalling of 4.6) without issue during installation (activation completed each time, with a message from firewall that "Activate.exe" was attempting to access the internet- which was allowed successfully).
I rebooted each time after installing WB5 beta.
The only issues I have seen are as follows:
In all three tests on both machines, I installed the WB5 program > rebooted > applied the "StealthOS" skin > unloaded WB using the config panel > attempted to use the Display Properties\Themes tab\Theme drop-down list to reapply the default Windows XP theme. In two of the three clean install procedures on both machines, I ran into an issue with the Themes tab preview, and the Appearance tab preview not displaying a shell image during the initial application of skin and unloading of WB5 beta (see images below).


In all but one of these cases, applying the theme (even though the shell was not displayed) resulted in no application of the default Windows XP theme, and a subsequent reboot of the system to determine if the theme would apply after rebooting - resulted in the StealthOS skin being applied (either completely, or partially).
The fix was to start WB config panel > apply the "Windows Classic" listing in WB > unload WB using link in config panel > use Display Properties\Themes tab\Theme drop-down list, to apply the Windows Classic theme > reboot > apply the Windows XP theme using the Display Properties\Themes tab\Theme drop-down list, after reboot. All instances of this work around were successful.
When this issue occured, it was only after the first attempt to apply and unload during each test procedure. After using the work around listed above, the StealthOS skin applied and unloaded as expected - with the Windows XP shell style displayed correctly in the Display Properties\Themes tab, allowing for the correct application of the Windows XP theme directly after unloading WindowBlinds.
In the one case of applying the Windows XP theme using the Display Properties\Themes tab\Theme drop-down list (even though the Windows XP shell was not displayed) the Windows XP theme applied only after rebooting, with the issues illustrated below.


The issue shown with Photoshop menus was persistent throughout the system and installed programs. The title bar retained the StealthOS sizing (pixel height and button sizes) as well. The Start menu issue was only seen in the menu itself, with the All Programs menu using the default "blue" color overlay for mouse-over.
In the first clean install test procedure (on both machines), I tested a few other skins as well (before using the "work around" listed above) and could not get WB5 to unload cleanly during the initial application and unloading test after installing WB5 beta.
In all cases, WB5 beta seemed to stabilize after a successful reapplication of the Windows XP theme, and then reapplying of a skin and use.
A couple of other issues were:
1 - When applying a system change (say changing the number of programs in the start menu via Start Menu Properties > Customize > OK > Apply), the taskbar will flicker (almost fail) for a second as the application is made.
2 - As I have mentioned in another post, Painter IX had an issue with version 4.6 - where the program's titlebar buttons, Min, Max\Restore, and Close - did not function. WB5 seems to have fixed this so that the program's titlebar buttons function (though this only applies to skins made for WB5, not skins made for WB4.6), but the same buttons on an inner "file" window still do not function in any skin.
That is about it for my part. I am still using, and will continue to use WB5 beta (with StealthOS skin) because all in all, these issues can be resolved in time and do not bother me because the work arounds are easy.
For a bit of fun, I have included a window puzzle titled: "Now where was I?"

Here are the Troubleshooting reports:
Desktop (Home built - ASUS MoBo w/ Intel 845G chipset, P4 2.5 Ghz processor, 400 Mhz FSB, 1.5 GB RAM (PC2100), Antec TruePower 380, Maxtor hard drives (7200 RPM), Plextor optical drives)
WindowBlinds 5 BETA Troubleshooting Report:
STATUS : WB+ SRV+ HLP+ UI+
WindowBlinds is installed correctly on this PC.
WindowBlinds appears to be activated on this PC
Your machine supports per pixel borders on WindowBlinds skins.
You have one monitor in total.
(Plug and Play Monitor) 1 is attached to RADEON X700 Series
'RADEON X700 Series Secondary ' also exists as device '\\.\DISPLAY2', but is not attached to the desktop.
'NetMeeting driver' also exists as device '\\.\DISPLAYV1', but is not attached to the desktop and is a mirror driver.
'RDPDD Chained DD' also exists as device '\\.\DISPLAYV2', but is not attached to the desktop and is a mirror driver.
Notebook: Dell Inspiron 9300 (Dell MoBo w/ Intel 915 chipset, Pentium M 1.6 Ghz, 533 Mhz FSB (PCI express), 2 GB RAM (PC2-4200), 40 GB Hitachi hard drive, Teac optical drive)
WindowBlinds 5 BETA Troubleshooting Report:
STATUS : WB+ SRV+ HLP+ UI+
WindowBlinds is installed correctly on this PC.
WindowBlinds appears to be activated on this PC
Your machine supports per pixel borders on WindowBlinds skins.
You have one monitor in total.
(Default Monitor) 1 is attached to ATI MOBILITY RADEON X300
'ATI MOBILITY RADEON X300 ' also exists as device '\\.\DISPLAY2', but is not attached to the desktop.
'NetMeeting driver' also exists as device '\\.\DISPLAYV1', but is not attached to the desktop and is a mirror driver.
'RDPDD Chained DD' also exists as device '\\.\DISPLAYV2', but is not attached to the desktop and is a mirror driver.
Thanks for the great fun, Stardock. ;)