After using the Universal Theme Patcher on my new laptop (running Windows 7 Ultimate 64-bit SP1) it seems that 3rd party visual styles/themes are not being applied to all applications, or in some cases only partially applied. I'm using the Gaia09 visual style, but this happens with any visual style I use, including the standard Aero style.
I've attached an image to show what I mean. On the left is Google Chrome with the Open dialog box opened. Except for the back/forward buttons in the location bar, it appears that the VS is being applied completely. On the right is Notepad++. The window frames around the main application and the Open dialog are using the VS, but the interior elements are not - they look like they're using the Classic theme. System-wide, this seems to be the case with many applications: they're either completely styled, or only their window borders and min/max/close buttons are being styled.
I've tried using the Universal Theme Patcher to patch both 64-bit and 32-bit system files. I've also tried the UxStyle Core service, and even TuneUp Utilities' built-in 3rd party theme support. After multiple patching and restoring attempts, I ran SFC /scannow to replace any affected system files, rebooted, repatched, etc. still without any luck.
I'd appreciate any help!