I'm running aero glass now with the ux theme register edit that allows all programs to have aero glass. On google chrome, I have a theme that themes the top of the window but it overwritten by aero glass. Is there a way to disable aero glass on google chrome only?

No, this is not possible unless Chrome provides you such option. Rendering engine does not know which window is drawn - it just have image and position.

So why not include a blacklist feature BM?

 

A simple editable text file in the aeroglass folder to disable glass for applications that seem incompatible.

 

A bit like vista basic mode.

Rendering engine does not know which window is drawn - it just have image and position.

It sounds more the fault of Chrome having certain capabilities. Having Aeroglass be written to disable it from working on Chrome is approaching it from the wrong angle.

Is it similar to how on Windows 7 with default Aero enabled, some programs when they are opened will cause Windows to change the theme to basic? I always run into this problem with Fireworks and never found a way to stop it from happening... although I haven't looked into it in a while.

It is the same situation as with blurring some window background - DWM is responsible for rendering only, so it must be instructed by external subject with functions DwmEnableBlurBehindWindow.

There is a function DwmSetWindowAttribute which can be used to remove some window from DWM rendering. So if someone wants to use it (e.g. for compatibility reasons) then he must call this function externally.

This is way above my skill level. I just thought it would be possible since Firefox isn't themed. I can live with the way it is now