Browser app windows by default are captured by the browser launcher. (Tested chrome/ chromium) After tweaking my launcher a bit, I can get it to properly capture app windows, but on if no browser is running. If the browser is opened after the app window, the app launcher captures the browser as well. Attached is my chrome launcher, a customized app launcher and a stock one.
ProblemType: Bug
DistroRelease: Ubuntu 12.04
Package: unity 5.2.0-0ubuntu4
ProcVersionSignature: Ubuntu 3.2.0-15.24-generic 3.2.5
Uname: Linux 3.2.0-15-generic x86_64
NonfreeKernelModules: nvidia
ApportVersion: 1.91-0ubuntu1
Architecture: amd64
CompizPlugins: [core,bailer,detection,composite,opengl,decor,obs,place,zoom,mousepoll,wall,imgsvg,text,move,thumbnail,vpswitch,session,commands,grid,imgpng,copytex,gnomecompat,resize,regex,imgjpeg,compiztoolbox,winrules,wobbly,animation,fade,workarounds,scale,resizeinfo,expo,ezoom,unityshell]
Date: Tue Feb 14 21:15:10 2012
InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Alpha amd64 (20120104)
SourcePackage: unity
UpgradeStatus: Upgraded to precise on 2012-02-12 (2 days ago)
And my gmail launcher