I took my original CD and make a few minor changes as a base to work tests off of (hereafter caled the Unattended CD). Basically setup unattended, removed a few components (languages, keyboards, tablet pc, media center, extra folders in the CD root), enabled the Uxtheme patch, disabled SFC, and integrated the one theme that I use, Royale Remixed. Then I burned it to a CD, and left the source on my hard drive.

Then I made a copy of it (so I dont have to copy from the CD each time), added my addons, setup tweaks, and left the rest alone, this one I'll call the fully tweaked CD.

When I finished installing the fully tweaked CD in MS VPC, everything worked, except for the theme. It loaded Windows Classic for the windows and taskbar, however the icons, background and cursors applied. When I looked at the display properties, the preview showed the same way that it does when you try to load an unsigned theme with an unpatched uxtheme. So I reloaded the fully tweaked version in nlite and looked at the patches page, and the uxtheme patch option was grayed out (as if the patch was applied).

As a quick test, I copied an unpatched uxtheme from my hard drive to the i386 folder of the fully tweaked cd, reloaded nLite and went back to the options page. The uxtheme patch option was able to be changed again.

Is it possible that nLite is unpatching the file?

I had and have the same problem, and I soleved that by manually installing uxtheme patcher application. I was wondering a lot of times what was the problem with the classic theme style untill I didn't tryied manually patching the uxtheme. But that doesn't makes me happy. By the way after nLite, I add a patched uxtheme compressed file, so I have another wonder, could that be the reason of uxtheme patching?
Any help is very welcome

Speeddymon,
I think your problem is that you nLited the same source more than once. You should always start with a fresh copy of your CD files/folders when you run nLite. The symptoms when you cheap are numerous, varied and often bizarre.
Enjoy, John.

It may be true that you shouldn't nlite the same source more than once on most occasions, but when I get a good build sometimes its hard not to.

Sounds like a simple-enough bug to fix though...