I'm having troubles with VS2012 and code opened in separate windows.
See this screenshot:

Main windows is open, another window is open (Source Control explorer is just an example for the screenshot, I get the same behavior with source code files). I used to get two items on the task bar for the Visual Studio. Now it is only one.
There is a setting for this:

But I can't get it undone. Every time I un-check this setting, I get a flicker of another item in task bar, but it goes away immediately. Then I go back to the same settings, the checkbox next to "Floating tab wells always stay on top" is checked again! That is very annoying.
I have traced the setting to a registry setting HKCU\Software\Microsoft\VisualStudio\11.0\DialogPage\Microsoft.VisualStudio.Platform.WindowManagement.Options.TabsAndWindowsOptionsPage\EnableIndependentTabWell and tried setting it to True (it was False) when VS was not running. But as soon as VS is started, this is switched to False again.
I have installed Power Tools for 2012 - that has some setting for custom tab wells, but I have removed that extension now. I believe the extension caused the issue, but why does it persist after un-installing of the extension? And how do I fix it?
UPD: When I run VS in safemode (via devenv /safemode) that setting is persisted. But as soon as I run normal mode, it is changed automatically.
UPD 2: Resharper 7.1 is to blame. This issue caused by this bug. To enable floating tabs going under do the following: this scenarios require switching the “always on top” option off, you can work around ReSharper behavior by mounting settings file to your ReShar