An additional property should be added for enabling the proxy on InternetExplorerDriver. Can you try with the following code for driver initialization:
DesiredCapabilities capabilities = new DesiredCapabilities();
capabilities.setCapability("ie.setProxyByServer", true);
final InternetExplorerDriver webDriver = new InternetExplorerDriver(
NLWebDriverFactory.addProxyCapabilitiesIfNecessary(capabilities));
webDriver.manage().timeouts().implicitlyWait(30, TimeUnit.SECONDS);