It worked for me in the 64bit version of IEDriverServer.
I just added the property requireWindowFocus with the value "true"
DesiredCapabilities capabilities = DesiredCapabilities.internetExplorer();
capabilities.setCapability(InternetExplorerDriver.INTRODUCE_FLAKINESS_BY_IGNORING_SECURITY_DOMAINS, true);
...
capabilities.setCapability("requireWindowFocus", true);
WebDriver driver = new InternetExplorerDriver(capabilities);