What hardware do you use ?
Can you provide a screenshot before and after ?

Can you provide output from glxinfo?

Thanks to Sinclair Yeh's detective work, it appears that the unity shell is disabling transparency when it finds "LLVM" in the GL_RENDERER string.

We've seen the same issue here with our latest VMware driver which includes the LLVM version in the GL_RENDERER string.  Sinclair found this code in the Unity shell in plugins/unityshell/src/unityshell.cpp:

  //In case of software rendering then enable lowgfx mode.
  std::string renderer = ANSI_TO_TCHAR(NUX_REINTERPRET_CAST(const char *, glGetString(GL_RENDERER)));

  if (renderer.find("Software Rasterizer") != std::string::npos ||
      renderer.find("Mesa X11") != std::string::npos ||
      renderer.find("LLVM") != std::string::npos ||
      renderer.find("on softpipe") != std::string::npos ||
      (getenv("UNITY_LOW_GFX_MODE") != NULL && atoi(getenv("UNITY_LOW_GFX_MODE")) == 1) ||
      optionGetLowGraphicsMode())
    {
      unity_settings_.SetLowGfxMode(true);
    }

It looks like Marek added code in the r600 driver to include LLVM version info in the renderer string too:

commit a3723fb9e32ab114dcffcf74946def92647c5f03
Author: Marek Olšák <marek.olsak@amd.com>
Date:   Mon Jul 20 00:15:59 2015 +0200

    gallium/radeon: add DRM and LLVM version to the renderer string
    
So, if the reporter of this bug is using the r600 driver, that could explain things.  He mentions a change in June/July.

Clearly, the unity code above is pretty dodgy.  I'll see if we can report the issue upstream.

BTW, I tried pinging the bug reporter but email to g9352248@trbvm.com bounces.

Done.  Created "old_gpg_id.txt" to show the previous ID, and also added new public key in my home directory.

thanks!

Ooops, wrong window.

Meant to say that I created a new Unity bug here:
https://bugs.launchpad.net/unity/+bug/1491555